CDXS / Codexis, Inc. - Pengajuan SECLaporan Tahunan, Pernyataan Proksi

Codexis, Inc.
US ˙ NasdaqGS ˙ US1920051067

Mga Batayang Estadistika
LEI 549300KGLM6CDPTVSE20
CIK 1200375
SEC Filings
All companies that sell securities in the United States must register with the Securities and Exchange Commission (SEC) and file reports on a regular basis. These reports include company annual reports (10K, 10Q), news updates (8K), investor presentations (found in 8Ks), insider trades (form 4), ownership reports (13D, and 13G), and reports related to the specific securities sold, such as registration statements and prospectus. This page shows recent SEC filings related to Codexis, Inc.
SEC Filings (Chronological Order)
Halaman ini menyediakan daftar lengkap dan kronologis dari Pengajuan SEC, tidak termasuk pengajuan kepemilikan yang kami sediakan di tempat lain.
August 13, 2025 S-8

As filed with the Securities and Exchange Commission on August 13, 2025

S-8 As filed with the Securities and Exchange Commission on August 13, 2025 Registration No.

August 13, 2025 EX-10.1

Second Amendment to the Codexis, Inc. 2019 Incentive Award Plan, as amended.

SECOND AMENDMENT TO THE CODEXIS, INC. 2019 INCENTIVE AWARD PLAN THIS SECOND AMENDMENT TO THE CODEXIS, INC. 2019 INCENTIVE AWARD PLAN (this “Amendment”) is made and adopted by Codexis, Inc. a Delaware corporation (the “Company”). Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to them in the Plan (as defined below). RECITALS WHEREAS, the Company maintains th

August 13, 2025 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2025 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis, I

August 13, 2025 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 13, 2025 Codexis, Inc. (Ex

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 13, 2025 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numb

August 13, 2025 EX-FILING FEES

Filing Fee Table.

Calculation of Filing Fee Tables S-8 CODEXIS, INC. Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee 1 Equity Common Stock, par value $0.0001 per share Other 8,000,000 $ 2.78 $ 22,240,000.00 0.0001531 $ 3,404.94 Total Offering Am

August 13, 2025 EX-99.1

Codexis Reports Second Quarter 2025 Financial Results Announces revenue of $15.3M vs $14.1M analyst consensus estimate Six presentations featured ECO Synthesis® platform at 2025 TIDES USA annual meeting, including three from leading CDMO collaborator

EX-99.1 Exhibit 99.1 Codexis Reports Second Quarter 2025 Financial Results Announces revenue of $15.3M vs $14.1M analyst consensus estimate Six presentations featured ECO Synthesis® platform at 2025 TIDES USA annual meeting, including three from leading CDMO collaborators $27.3M raised via ATM facility and Innovatus loan to support expansion of ECO Synthesis REDWOOD CITY, Calif., August 13, 2025 —

June 11, 2025 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 10, 2025 Codexis, Inc. (Exac

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 10, 2025 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

May 14, 2025 EX-99.1

Codexis Reports First Quarter 2025 Financial Results Secured first revenue-generating contract for ECO Synthesis™ manufacturing services Company reiterates full-year financial guidance Six presentations to feature the ECO Synthesis platform at upcomi

EX-99.1 Exhibit 99.1 Codexis Reports First Quarter 2025 Financial Results Secured first revenue-generating contract for ECO Synthesis™ manufacturing services Company reiterates full-year financial guidance Six presentations to feature the ECO Synthesis platform at upcoming TIDES USA annual meeting, including three from leading CDMO collaborators REDWOOD CITY, Calif., May 14, 2025 — Codexis, Inc. (

May 14, 2025 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 14, 2025 Codexis, Inc. (Exact

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 14, 2025 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number)

May 14, 2025 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2025 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis,

May 14, 2025 EX-10.1

Acquisition Agreement by and among the Company, Societé des Produits Nestlé S.A., formerly known as Nestec Ltd. ("Nestlé Health Science"), effective as of

CONFIDENTIAL AMENDMENT NO. 1 TO AQUISITION AGREEMENT This amendment (“Amendment”) is entered into as of February 28, 2025 (the “Amendment Effective Date”) by and between Codexis, Inc., with offices at 200 Penobscot Dr., Redwood City, CA 94063 (“Seller” or “Codexis”) and Société des Produits Nestlé S.A., with offices at 55 Avenue Nestlé, 1800 Vevey, Switzerland (“Buyer” or “NHSc”). WHEREAS, Seller

April 24, 2025 DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

DEFA14A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Pro

April 24, 2025 DEF 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Defi

April 9, 2025 8-K

Regulation FD Disclosure

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 4, 2025 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

April 9, 2025 EX-99.1

Codexis Announces Byron Dorgan to Retire from Board of Directors

Exhibit 99.1 Codexis Announces Byron Dorgan to Retire from Board of Directors REDWOOD CITY, Calif., April 9, 2025 — Codexis, Inc. (NASDAQ: CDXS), a leading provider of enzymatic solutions for efficient and scalable therapeutics manufacturing, today announced that Byron Dorgan will retire from the Company’s Board of Directors when his current term ends at the 2025 Annual Meeting of Stockholders. Mr

March 31, 2025 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 28, 2025 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numbe

February 27, 2025 EX-99.1

Codexis Reports Fourth Quarter and Fiscal Year 2024 Financial Results Total revenue of $59.3 million for the fiscal year ended December 31, 2024 Expect double digit growth for total revenue in 2025 2025 to demonstrate acceleration of commercial growt

EX-99.1 Exhibit 99.1 Codexis Reports Fourth Quarter and Fiscal Year 2024 Financial Results Total revenue of $59.3 million for the fiscal year ended December 31, 2024 Expect double digit growth for total revenue in 2025 2025 to demonstrate acceleration of commercial growth through double-stranded RNA ligase and GLP-grade siRNA material; expect to secure GMP scale-up partner REDWOOD CITY, Calif., Fe

February 27, 2025 EX-10.1J

, by and between the Company and Metropolitan Life Insurance Company.

[***] Certain marked information has been omitted from this exhibit because it is both not material and is the type that the Registrant treats as private or confidential.

February 27, 2025 8-K

Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 27, 2025 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 27, 2025 EX-10.16C

, 2024, by and between the Company and Innovatus Life Sciences Fund I, LP.

SECOND AMENDMENT TO LOAN AND SECURITY AGREEMENT This SECOND AMENDMENT TO LOAN AND SECURITY AGREEMENT (this “Agreement”) is entered into as of December 20, 2024, by and among INNOVATUS LIFE SCIENCES LENDING FUND I, LP, a Delaware limited partnership (together with its successors and assigns, “Innovatus”), as collateral agent (in such capacity, together with its successors and assigns in such capacity, “Collateral Agent”), the Lenders listed on Schedule 1.

February 27, 2025 EX-19.1

odexis Insider Trading P

INSIDER TRADING COMPLIANCE PROGRAM Approved by the Company’s Board of Directors on May 9, 2024 This Insider Trading Compliance Program (the “Program”) consists of six sections: Section I provides an overview; Section II sets forth Codexis, Inc.

February 27, 2025 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended: December 31, 2024 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission File No.: 001-34705 Codexis, Inc.

February 27, 2025 EX-10.15C

and Consulting Agreement by and between the Company and Sriram Ryali dated October 16, 2024

[*] = CERTAIN MARKED INFORMATION HAS BEEN OMITTED FROM THIS EXHIBIT BECAUSE IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL.

January 16, 2025 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 14, 2025 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

November 12, 2024 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 7, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

November 12, 2024 EX-3.1

Second Amended and Restated Bylaws of Codexis, Inc. effective as of November 7, 2024 (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on November 12, 2024).

Exhibit 3.1 AMENDED AND RESTATED BYLAWS OF CODEXIS, INC. (a Delaware corporation) November 7, 2024 TABLE OF CONTENTS Page ARTICLE I - CORPORATE OFFICES 1 1.1 REGISTERED OFFICE 1 1.2 OTHER OFFICES 1 ARTICLE II - MEETINGS OF STOCKHOLDERS 1 2.1 PLACE OF MEETINGS 1 2.2 ANNUAL MEETING 1 2.3 SPECIAL MEETING 1 2.4 ADVANCE NOTICE PROCEDURES FOR BUSINESS BROUGHT BEFORE A MEETING 2 2.5 ADVANCE NOTICE PROCED

October 31, 2024 EX-10.6

Change in Control Severance Agreement by and between the Company and

CODEXIS, INC. CHANGE OF CONTROL SEVERANCE AGREEMENT This Change of Control Severance Agreement (the “Agreement”) is made and entered into by and between Alison Moore (the “Executive”) and Codexis, Inc., a Delaware corporation (the “Company”), effective as of the latest date set forth by the signatures of the parties hereto below (the “Effective Date”). R E C I T A L S AIt is expected that the Comp

October 31, 2024 EX-99.1

Codexis Reports Third Quarter 2024 Financial Results Quarter Highlights Include Key Additions to Management Team and Extension of Cash Runway into 2027 with $31M Raise via ATM Facility Company Reiterates Full-year Financial Guidance; On Track to Achi

Exhibit 99.1 Codexis Reports Third Quarter 2024 Financial Results Quarter Highlights Include Key Additions to Management Team and Extension of Cash Runway into 2027 with $31M Raise via ATM Facility Company Reiterates Full-year Financial Guidance; On Track to Achieve Product Revenue Growth of at Least 10% vs. FY2023 Excluding Enzyme Sales Related to PAXLOVID™ REDWOOD CITY, Calif., October 31, 2024

October 31, 2024 EX-10.5

Offer Letter by and between the Company and

Codexis, Inc. 200 Penobscot Drive Redwood City, CA 94063 Tel: +1 (650) 421-8100 Fax: +1 (650) 421-8102 www.codexis.com September 19, 2024 Dr. Alison Moore, Ph.D. Dear Alison, On behalf of Codexis, Inc. (“Codexis” or the “Company”), I am pleased to extend to you this offer of employment as Executive Vice President, Chief Technical Officer reporting to Stephen Dilly, Chairman, President and Chief Ex

October 31, 2024 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2024 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codex

October 31, 2024 8-K

Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 31, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

October 31, 2024 EX-10.3

Offer Letter by and between the Company and

Codexis, Inc. 200 Penobscot Drive Redwood City, CA 94063 Tel: +1 (650) 421-8100 Fax: +1 (650) 421-8102 www.codexis.com September 30, 2024 Georgia Erbez Dear Georgia, On behalf of Codexis, Inc. (“Codexis” or the “Company”), I am pleased to extend to you this offer of employment as Chief Financial Officer reporting to Stephen Dilly, Chairman, President and Chief Executive Officer (the “CEO”). Your p

October 31, 2024 EX-10.2

(incorporated by reference to Exhibit 10.2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 20

FIRST AMENDMENT TO CODEXIS, INC. 2023 EMPLOYEE STOCK PURCHASE PLAN WHEREAS, Codexis, Inc., a Delaware corporation (the “Company”), has heretofore adopted the Codexis, Inc. 2023 Employee Stock Purchase Plan (the “Plan”); and WHEREAS, the Company wishes to amend the Plan to allow participants under the Plan to increase or decrease the amount of payroll deductions elected by such participants during

October 31, 2024 EX-10.4

Change in Control Severance Agreement by and between the Company and

CODEXIS, INC. CHANGE OF CONTROL SEVERANCE AGREEMENT This Change of Control Severance Agreement (the “Agreement”) is made and entered into by and between Georgia Erbez (the “Executive”) and Codexis, Inc., a Delaware corporation (the “Company”), effective as of the latest date set forth by the signatures of the parties hereto below (the “Effective Date”). R E C I T A L S A.It is expected that the Co

October 22, 2024 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 16, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

October 2, 2024 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 30, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File N

September 26, 2024 SC 13G

CDXS / Codexis, Inc. / Casdin Capital, LLC Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No.

September 18, 2024 SC 13G/A

CDXS / Codexis, Inc. / Opaleye Management Inc. Passive Investment

SC 13G/A 1 formsc13ga.htm UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Codexis Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 192005106 (CUSIP Number) James Silverman, One Boston Place, 26th Floor, Boston, MA 02108 (Name, Address, and Telephone Number

August 9, 2024 S-8

As filed with the Securities and Exchange Commission on August 9, 2024

As filed with the Securities and Exchange Commission on August 9, 2024 Registration No.

August 9, 2024 EX-4.1

Codexis, Inc. 2024 Inducement Plan.

Exhibit 4.1 CODEXIS, INC. 2024 INDUCEMENT PLAN 1. PURPOSE OF PLAN The purpose of this Codexis, Inc. 2024 Inducement Plan (this “Plan”) of Codexis, Inc., a Delaware corporation (the “Company”), is to advance the interests of the Company by providing a material inducement for the best available individuals to join the Company and its Subsidiaries as employees by affording such individuals an opportu

August 9, 2024 EX-FILING FEES

Filing Fee Table.

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Codexis, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common Stock, par value $0.0001 pe

August 8, 2024 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2024 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis, I

August 8, 2024 EX-10.1

Amendment No. 1 to the Loan and Security Agreement by and between the Company and Innovatus Life Sciences Fund I, LP., effective as of February 13, 2024.

CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL.

August 8, 2024 EX-99.1

Codexis Reports Second Quarter 2024 Financial Results Company Reiterates Full-year Financial Guidance; On Track to Achieve Product Revenue Growth of at Least 10% vs. FY2023 Excluding Enzyme Sales Related to PAXLOVID™ Anticipate Entering First Technic

Exhibit 99.1 Codexis Reports Second Quarter 2024 Financial Results Company Reiterates Full-year Financial Guidance; On Track to Achieve Product Revenue Growth of at Least 10% vs. FY2023 Excluding Enzyme Sales Related to PAXLOVID™ Anticipate Entering First Technical Collaboration for ECO Synthesis™ Manufacturing Platform by End of Year REDWOOD CITY, Calif., August 8, 2024 - Codexis, Inc. (NASDAQ: C

August 8, 2024 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 8, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numbe

July 12, 2024 SC 13G

CDXS / Codexis, Inc. / Opaleye Management Inc. Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Codexis Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 192005106 (CUSIP Number) James Silverman, One Boston Place, 26th Floor, Boston, MA 02108 (Name, Address, and Telephone Number of Person Authorized to Re

June 13, 2024 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 11, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

May 14, 2024 424B5

Up to $75,000,000 Codexis, Inc. Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No.333-279082 PROSPECTUS Up to $75,000,000 Codexis, Inc. Common Stock We have entered into a Controlled Equity OfferingSM sales agreement, or the sales agreement, with Cantor Fitzgerald & Co., or Cantor, relating to the sale of shares of our common stock, par value $0.0001 per share, offered by this prospectus. In accordance with the

May 14, 2024 EX-99.1

Codexis Presents Groundbreaking Enzymatic Synthesis Data at TIDES USA Annual Meeting

Exhibit 99.1 Codexis Presents Groundbreaking Enzymatic Synthesis Data at TIDES USA Annual Meeting REDWOOD CITY, Calif., May 14, 2024 — Codexis, Inc. (NASDAQ: CDXS), a leading enzyme engineering company, today announced it has successfully synthesized an oligonucleotide via an enzymatic route to support RNA-based therapeutics manufacturing. Data highlighting this historic manufacturing milestone ar

May 14, 2024 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 14, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number)

May 10, 2024 CORRESP

CODEXIS, INC. 200 Penobscot Drive Redwood City, California 94063 (650) 421-8100 May 10, 2024

CODEXIS, INC. 200 Penobscot Drive Redwood City, California 94063 (650) 421-8100 May 10, 2024 VIA EDGAR SUBMISSION U.S. Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attention: Benjamin Richie Re: Codexis, Inc. Registration Statement on Form S-3 File No. 333-279082 Acceleration Request Requested Date: May 14, 2024 Requested Time: 9:00 A

May 2, 2024 EX-99.1

Codexis Reports First Quarter 2024 Financial Results Q1 Total Revenue Up 32% Year-over-year, Including Product Revenue Up 14%; Company Reiterates 2024 Financial Guidance First Substantial Order for dsRNA Ligase Received from Large Pharma Customer Com

Exhibit 99.1 Codexis Reports First Quarter 2024 Financial Results Q1 Total Revenue Up 32% Year-over-year, Including Product Revenue Up 14%; Company Reiterates 2024 Financial Guidance First Substantial Order for dsRNA Ligase Received from Large Pharma Customer Company is in Final Stages of Enzymatically Synthesizing a Full-Length Oligonucleotide with ECO Synthesis™ Manufacturing Platform and will P

May 2, 2024 EX-1.2

Controlled Equity OfferingSM Sales Agreement, dated May 2, 2024, between Codexis, Inc. and Cantor Fitzgerald & Co.

Exhibit 1.2 Codexis, Inc. Shares of Common Stock (par value $0.0001 per share) Controlled Equity OfferingSM Sales Agreement May 2, 2024 Cantor Fitzgerald & Co. 110 East 59th Street, 6th Floor New York, NY 10022 Ladies and Gentlemen: Codexis, Inc., a Delaware corporation (the “Company”), confirms its agreement (this “Agreement”) with Cantor Fitzgerald & Co. (the “Agent”), as follows: 1. Issuance an

May 2, 2024 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2024 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis,

May 2, 2024 EX-FILING FEES

Filing Fee Table

Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) Codexis, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered and Carry Forward Securities Security Type Security Class Title Fee Calculation or Carry Forward Rule Amount Registered Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Carry For

May 2, 2024 EX-4.2

Form of Indenture

Exhibit 4.2 CODEXIS, INC. INDENTURE Dated as of , 20 [ ] Trustee TABLE OF CONTENTS Page ARTICLE I. DEFINITIONS AND INCORPORATION BY REFERENCE 2 Section 1.1. Definitions 2 Section 1.2. Other Definitions 5 Section 1.3. Incorporation by Reference of Trust Indenture Act 6 Section 1.4. Rules of Construction 6 ARTICLE II. THE SECURITIES 6 Section 2.1. Issuable in Series 6 Section 2.2. Establishment of T

May 2, 2024 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 2, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number)

May 2, 2024 S-3

As filed with the Securities and Exchange Commission on May 2, 2024

Table of Contents As filed with the Securities and Exchange Commission on May 2, 2024 Registration No.

April 25, 2024 DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy State

April 25, 2024 DEF 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Defi

March 6, 2024 EX-16.1

Letter from BDO USA, P.C., dated March 5, 2024

Exhibit 16.1 March 5, 2024 Securities and Exchange Commission 100 F Street N.E. Washington, D.C. 20549 We have been furnished with a copy of the response to Item 4.01 of Form 8-K for the event that occurred on February 29, 2024, to be filed by our former client, Codexis, Inc. We agree with the statements made in response to that Item insofar as they relate to our Firm. Very truly yours, /s/ BDO US

March 6, 2024 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 29, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 28, 2024 EX-10.17

(incorporated by reference to Exhibit 10.17 to the Company's Annual Report on Form 10-K for the year ended December 31, 2023, filed on February 28, 2024).

[*] = CERTAIN MARKED INFORMATION HAS BEEN OMITTED FROM THIS EXHIBIT BECAUSE IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL.

February 28, 2024 EX-10.11

Societé des Produits Nestlé S.A., formerly known as Nestec Ltd. ("Nestlé Health Science"),

CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL.

February 28, 2024 EX-99.1

Codexis Reports Fourth Quarter and Fiscal Year 2023 Financial Results Anticipate 2024 Product Revenue Growth of at Least 10% vs. 2023 Excluding Enzyme Sales Related to PAXLOVID™ Recently Announced Debt Financing Reinforces Strong Financial Position w

Exhibit 99.1 Codexis Reports Fourth Quarter and Fiscal Year 2023 Financial Results Anticipate 2024 Product Revenue Growth of at Least 10% vs. 2023 Excluding Enzyme Sales Related to PAXLOVID™ Recently Announced Debt Financing Reinforces Strong Financial Position with Projected Runway Through Expected Positive Cash-flow Around End of 2026 2024 to Focus on Securing Early Access Customers for ECO Synt

February 28, 2024 EX-4.4

Description of Codexis' Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934.

Exhibit 4.4 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 As of February 28, 2024, Codexis, Inc. (“we,” “us” or “our”) had one class of securities registered under Section 12 of the Securities Exchange Act of 1934, as amended: our common stock, $0.0001 par value per share (“common stock”). Description of Common Stock The followi

February 28, 2024 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): February 28, 2024 Codexis, Inc. (

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): February 28, 2024 Codexis, Inc. (Exact name of Registrant as Specified in its Charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 28, 2024 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended: December 31, 2023 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission File No.: 001-34705 Codexis, Inc.

February 28, 2024 EX-97.1

odexis, Inc. Clawback Policy effective August

CODEXIS, INC. POLICY ON RECOUPMENT OF INCENTIVE COMPENSATION Introduction The Board of Directors (the “Board”) of Codexis, Inc. (the “Company”) has adopted this Policy on Recoupment of Incentive Compensation (this “Policy”), which provides for the recoupment of compensation in certain circumstances in the event of a restatement of financial results by the Company. This Policy shall be interpreted

February 16, 2024 8-K

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 13, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 14, 2024 SC 13G/A

CDXS / Codexis, Inc. / Nantahala Capital Management, LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 11)* Codexis, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 192005106 (CUSIP Number) December 31, 2023 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the rule pu

February 13, 2024 EX-4.1

Form of Warrant to Purchase Common Stock for Codexis, Inc., issued pursuant to the Loan and Security Agreement by and between the Company and Innovatus Life Sciences Fund I, LP. (incorporated by reference to Exhibit 4.1 to the Company’s Current Report on Form 8-K, filed on February 13, 2024).

Exhibit 4.1 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED (I) UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR (II) WITHOUT AN OPINION OF COUNSEL, IN FORM AND

February 13, 2024 SC 13G/A

CDXS / Codexis, Inc. / VANGUARD GROUP INC - SCHEDULE 13G/A Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 2)* Name of issuer: Codexis Inc Title of Class of Securities: Common Stock CUSIP Number: 192005106 Date of Event Which Requires Filing of this Statement: December 29, 2023 Check the appropriate box to designate the rule pursuant to which this Schedule is filed: ☒ Rule 13

February 13, 2024 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 13, 2024 Codexis, Inc. (

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 13, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 9, 2024 EX-3.1

Amended and Restated Bylaws of Codexis, Inc. effective as of February 8, 2024 (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K filed on February 9, 2024).

Exhibit 3.1 AMENDED AND RESTATED BYLAWS OF CODEXIS, INC. (a Delaware corporation) February 8, 2024 TABLE OF CONTENTS Page ARTICLE I - CORPORATE OFFICES 1 1.1 REGISTERED OFFICE 1 1.2 OTHER OFFICES 1 ARTICLE II - MEETINGS OF STOCKHOLDERS 1 2.1 PLACE OF MEETINGS 1 2.2 ANNUAL MEETING 1 2.3 SPECIAL MEETING 1 2.4 ADVANCE NOTICE PROCEDURES FOR BUSINESS BROUGHT BEFORE A MEETING 2 2.5 ADVANCE NOTICE PROCED

February 9, 2024 8-K

Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 8, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

January 9, 2024 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 9, 2024 Codexis, Inc. (Ex

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 9, 2024 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numb

December 27, 2023 8-K

Entry into a Material Definitive Agreement, Termination of a Material Definitive Agreement

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 27, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

November 3, 2023 EX-10.1

Assignment and Assumption of Lease by and between the Company and Vaxcyte, Inc. dated as of September 1, 2023 (incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2023, filed on November 3, 2023).

ASSIGNMENT AND ASSUMPTION OF LEASE This ASSIGNMENT AND ASSUMPTION OF LEASE (this “Assignment”) is executed as of September 1, 2023 by and between CODEXIS, INC, a Delaware corporation (“Assignor”) and VAXCYTE, INC.

November 3, 2023 EX-10.2

Consent to Assignment and First Amendment to Lease Agreement by and between the Company, Vaxcyte Inc. and ARE-San Francisco No. 63, LLC dated as of September 6, 2023 (incorporated by reference to Exhibit 10.

CONSENT TO ASSIGNMENT AND FIRST AMENDMENT This Consent to Assignment and First Amendment (this “Consent”) is made as of September , 2023, by ARE-SAN FRANCISCO NO.

November 3, 2023 8-K/A

Material Impairments, Costs Associated with Exit or Disposal Activities

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K/A (Amendment No. 1) CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 2, 2023 (July 20, 2023) Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of

November 3, 2023 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2023 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codex

November 2, 2023 EX-99.1

Codexis Reports Third Quarter 2023 Financial Results Company Remains on Track to Demonstrate Gram-Scale Synthesis with ECO Synthesis™ Platform for RNAi Therapeutics Production by End of Year Strong Financial Position Enables Projected Runway to Expec

Exhibit 99.1 Codexis Reports Third Quarter 2023 Financial Results Company Remains on Track to Demonstrate Gram-Scale Synthesis with ECO Synthesis™ Platform for RNAi Therapeutics Production by End of Year Strong Financial Position Enables Projected Runway to Expected Positive Cash Flow Around End of 2026 Company to Host Virtual ECO Synthesis™ Platform-Focused KOL Event on December 8, 2023, featurin

November 2, 2023 8-K

Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 2, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

September 22, 2023 8-K

Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 21, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File N

September 22, 2023 EX-3.1

Amended and Restated Bylaws of Codexis, Inc., effective as of September 21, 2023

Exhibit 3.1 AMENDED AND RESTATED BYLAWS OF CODEXIS, INC. (a Delaware corporation) September 21, 2023 TABLE OF CONTENTS Page ARTICLE I - CORPORATE OFFICES 1 1.1 REGISTERED OFFICE 1 1.2 OTHER OFFICES 1 ARTICLE II - MEETINGS OF STOCKHOLDERS 1 2.1 PLACE OF MEETINGS 1 2.2 ANNUAL MEETING 1 2.3 SPECIAL MEETING 1 2.4 ADVANCE NOTICE PROCEDURES FOR BUSINESS BROUGHT BEFORE A MEETING 2 2.5 ADVANCE NOTICE PROC

September 7, 2023 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 1, 2023 Codexis, Inc. (

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 1, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

August 3, 2023 EX-3.3

Certificate of Amendment to the Amended and Restated Certificate of Incorporation of Codexis, Inc., filed with the Secretary of the State of the State of Delaware on June 14, 2023 (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on June 16, 2023).

CERTIFICATE OF AMENDMENT TO NINTH AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CODEXIS, INC.

August 3, 2023 EX-FILING FEES

Filing Fee Table.

Exhibit 107.1 Calculation of Filing Fee Tables Form S-8 (Form Type) Codexis, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered (1) Proposed Maximum Offering Price Per Share (2) Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common Stock, $0.0001 par

August 3, 2023 S-8

As filed with the Securities and Exchange Commission on August 3, 2023

S-8 As filed with the Securities and Exchange Commission on August 3, 2023 Registration No.

August 3, 2023 EX-10.1

Codexis, Inc. 2023 Employee Stock Purchase Plan (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on June 16, 2023).

Exhibit 10.1 CODEXIS, INC. 2023 EMPLOYEE STOCK PURCHASE PLAN ARTICLE 1 PURPOSE The Plan’s purpose is to assist employees of the Company and its Designated Subsidiaries in acquiring a stock ownership interest in the Company, and to help such employees provide for their future security and to encourage them to remain in the employment of the Company and its Subsidiaries. The Plan consists of two com

August 3, 2023 EX-99.1

Codexis Reports Second Quarter 2023 Financial Results Company Recently Announced Enhanced Strategic Focus and Portfolio Prioritization Anticipate Demonstrating Gram-Scale Synthesis of ECO Synthesis™ Technology for RNAi Therapeutics Production by End

Exhibit 99.1 Codexis Reports Second Quarter 2023 Financial Results Company Recently Announced Enhanced Strategic Focus and Portfolio Prioritization Anticipate Demonstrating Gram-Scale Synthesis of ECO Synthesis™ Technology for RNAi Therapeutics Production by End of Year Projected Cash Runway to Mid-2026 Funds Important ECO Synthesis™ Milestones Through Commercialization REDWOOD CITY, Calif., Augus

August 3, 2023 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 3, 2023 Codexis, Inc. (Exa

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 3, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numbe

August 3, 2023 EX-FILING FEES

Filing Fee Table.

Exhibit 107.1 Calculation of Filing Fee Tables Form S-8 (Form Type) Codexis, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered (1) Proposed Maximum Offering Price Per Share (2) Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common Stock, $0.0001 par

August 3, 2023 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2023 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis, I

August 3, 2023 EX-10.2

Amendment to the Codexis, Inc. 2019 Incentive Award Plan (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on June 16, 2023).

AMENDMENT TO THE CODEXIS, INC. 2019 INCENTIVE AWARD PLAN THIS AMENDMENT TO THE CODEXIS, INC. 2019 INCENTIVE AWARD PLAN (this “Amendment”) is made and adopted by Codexis, Inc. a Delaware corporation (the “Company”). Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to them in the Plan (as defined below). RECITALS WHEREAS, the Company maintains the Codexis, Inc

August 3, 2023 S-8

As filed with the Securities and Exchange Commission on August 3, 2023

As filed with the Securities and Exchange Commission on August 3, 2023 Registration No.

July 20, 2023 EX-99.1

Codexis Announces Enhanced Strategic Focus and Extends Projected Cash Runway to Mid-2026 Organization Streamlined to Focus on Continued Advancement and Commercialization of ECO Synthesis™ Platform for RNAi Therapeutics Production Codexis Expects its

Exhibit 99.1 Codexis Announces Enhanced Strategic Focus and Extends Projected Cash Runway to Mid-2026 Organization Streamlined to Focus on Continued Advancement and Commercialization of ECO Synthesis™ Platform for RNAi Therapeutics Production Codexis Expects its Pharmaceutical Manufacturing Business to Return to Growth in 2024 Company Reiterates 2023 Product Revenue Guidance and Announces Prelimin

July 20, 2023 8-K

Financial Statements and Exhibits, Material Impairments, Costs Associated with Exit or Disposal Activities, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 20, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

June 16, 2023 EX-10.1

Codexis, Inc. 2023 Employee Stock Purchase Plan.

EX-10.1 Exhibit 10.1 CODEXIS, INC. 2023 EMPLOYEE STOCK PURCHASE PLAN ARTICLE 1 PURPOSE The Plan’s purpose is to assist employees of the Company and its Designated Subsidiaries in acquiring a stock ownership interest in the Company, and to help such employees provide for their future security and to encourage them to remain in the employment of the Company and its Subsidiaries. The Plan consists of

June 16, 2023 EX-10.2

Amendment to the Codexis, Inc. 2019 Incentive Award Plan.

EX-10.2 Exhibit 10.2 AMENDMENT TO THE CODEXIS, INC. 2019 INCENTIVE AWARD PLAN THIS AMENDMENT TO THE CODEXIS, INC. 2019 INCENTIVE AWARD PLAN (this “Amendment”) is made and adopted by Codexis, Inc. a Delaware corporation (the “Company”). Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to them in the Plan (as defined below). RECITALS WHEREAS, the Company maint

June 16, 2023 EX-3.1

Certificate of Amendment to the Amended and Restated Certificate of Incorporation of Codexis, Inc., filed with the Secretary of the State of the State of Delaware on June 14, 2023 (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on June 16, 2023).

EX-3.1 Exhibit 3.1 CERTIFICATE OF AMENDMENT TO NINTH AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CODEXIS, INC. The undersigned duly authorized officer of Codexis, Inc., a Delaware corporation, hereby certifies the following: ONE: The original name of this corporation is Codexis, Inc. and the date of filing the original Certificate of Incorporation of this corporation with the Secretary of

June 16, 2023 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 13, 2023 Codexis, Inc. (Exac

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 13, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

May 4, 2023 EX-10.1

Termination of the Loan and Security Agreement by and between the Company and Western Alliance Bank dated as of March 13, 2023.

March 13, 2023 CODEXIS, INC. 200 Penobscot Drive Redwood City, CA 94063 Attn: Sri Ryali, CFO FAX: [***] EMAIL: [***] Loan Number: 121143260 Borrower: Codexis, Inc. Reference is made to that certain Loan and Security Agreement, dated June 30, 2017, by and between Western Alliance Bank, an Arizona corporation (“Bank”) and Codexis, Inc., a Delaware corporation ("Borrower") (as amended from time to ti

May 4, 2023 EX-99.1

Codexis Reports First Quarter 2023 Financial Results CDX-7108 Clinical Development Program Remains on Track Estimated Cash Runway Through End of 2024 Funds Important Upcoming Milestones Company Reiterates 2023 Total Revenue Guidance with Adjustments

Exhibit 99.1 Codexis Reports First Quarter 2023 Financial Results CDX-7108 Clinical Development Program Remains on Track Estimated Cash Runway Through End of 2024 Funds Important Upcoming Milestones Company Reiterates 2023 Total Revenue Guidance with Adjustments to Product vs. R&D Revenue Mix and Range on Gross Margin REDWOOD CITY, Calif., May 4, 2023 - Codexis, Inc. (NASDAQ: CDXS), a leading enzy

May 4, 2023 POS EX

As filed with the Securities and Exchange Commission on May 4, 2023

POS EX As filed with the Securities and Exchange Commission on May 4, 2023 Registration No.

May 4, 2023 EX-10.2

Amendment No. 3 to the Enzyme Supply Agreement by and between the Company and Pfizer Ireland Pharmaceuticals,

AMENDMENT NO. 3 TO ENZYME SUPPLY AGREEMENT This Amendment No. 3 to Enzyme Supply Agreement (this “Amendment”) is made as of March 30, 2023 (the “Amendment Effective Date”), between Codexis, Inc., a Delaware corporation having its principal offices at 200 Penobscot Drive, Redwood City, California 94063 (“Codexis”) and Pfizer Ireland Pharmaceuticals, an Ireland corporation, with its principal place

May 4, 2023 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 4, 2023 Codexis, Inc. (Exact

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 4, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number)

May 4, 2023 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2023 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis,

April 27, 2023 DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

DEFA14A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Pro

April 27, 2023 DEF 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Defi

April 17, 2023 PRE 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☒ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Defi

April 4, 2023 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): March 29, 2023 Codexis, Inc. (Exa

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): March 29, 2023 Codexis, Inc. (Exact name of Registrant as Specified in its Charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numbe

February 28, 2023 POS AM

As filed with the Securities and Exchange Commission on February 27, 2023

POS AM 1 d377820dposam.htm POS AM Table of Contents As filed with the Securities and Exchange Commission on February 27, 2023 Registration No. 333-255926 UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 POST-EFFECTIVE AMENDMENT NO. 2 to FORM S-3 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 CODEXIS, INC. (Exact name of Registrant as specified in its charter) Delawa

February 27, 2023 EX-10.23A

(incorporated by reference to Exhibit 10.13A to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

December 27, 2022 Sri Ryali Dear Sri, Codexis, Inc. 200 Penobscot Drive Redwood City, CA 94063 Tel: +1 (650) 421-8100 Fax: +1 (650) 421-8102 www.codexis.com On behalf of Codexis, Inc. (“Codexis” or the “Company”), I am pleased to extend to you this offer of employment as Chief Financial Officer reporting to Stephen Dilly, President and Chief Executive Officer. Your position is a full-time and exem

February 27, 2023 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended: December 31, 2022 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission File No.: 001-34705 Codexis, Inc.

February 27, 2023 EX-10.19B

Amendment No. 1 to the Enzyme Supply Agreement by and between the Company and Pfizer Ireland Pharmaceuticals, effective as of December 19, 2022.

Execution Version AMENDMENT NO. 1 TO ENZYME SUPPLY AGREEMENT This Amendment No. 1 to Enzyme Supply Agreement (this “Amendment No. 1”) is made as of December 19, 2022 (the “Amendment No. 1 Effective Date”), between Codexis, Inc., a Delaware corporation having its principal offices at 200 Penobscot Drive, Redwood City, California 94063 (“Codexis”) and Pfizer Ireland Pharmaceuticals, an Irish corpora

February 27, 2023 POSASR

As filed with the Securities and Exchange Commission on February 27, 2023

POSASR 1 d466048dposasr.htm POSASR Table of Contents As filed with the Securities and Exchange Commission on February 27, 2023 Registration No. 333-255926 UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 POST-EFFECTIVE AMENDMENT NO. 1 to FORM S-3 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 CODEXIS, INC. (Exact name of Registrant as specified in its charter) Delaw

February 27, 2023 EX-FILING FEES

Filing Fee Table (incorporated by reference to Exhibit 107.1 to the Company’s Registration Statement on Form S-3, filed on February 27, 2023).

EX-FILING FEES Exhibit 107.1 Calculation of Filing Fee Tables Form S-3 (Form Type) Codexis, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered and Carry Forward Securities Security Type Security Class Title Fee Calculation or Carry Forward Rule Amount Registered Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registrat

February 27, 2023 EX-10.4

Form of Indemnification Agreement between the Company and each of its directors, officers and certain employees (incorporated by reference to Exhibit 10.4 to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

CODEXIS, INC. INDEMNIFICATION AGREEMENT This Indemnification Agreement (“Agreement”) is effective as of December 16, 2022, by and between Codexis, Inc., a Delaware corporation (the “Company”), and [INDEMNITEE] (“Indemnitee”). A.The Company recognizes the continued difficulty in obtaining liability insurance for its directors, officers, employees, controlling persons, fiduciaries and other agents a

February 27, 2023 EX-10.23B

Change in Control Severance Agreement by and between the Company and Sriram Ryali dated January 27, 2023

CODEXIS, INC. CHANGE OF CONTROL SEVERANCE AGREEMENT This Change of Control Severance Agreement (the “Agreement”) is made and entered into by and between Sri Ryali (the “Executive”) and Codexis, Inc., a Delaware corporation (the “Company”), effective as of the latest date set forth by the signatures of the parties hereto below (the “Effective Date”). R E C I T A L S A.It is expected that the Compan

February 27, 2023 EX-10.8B

to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

TRANSITION AND SEPARATION AGREEMENT This Transition and Separation Agreement (the “Agreement”) by and between Ross Taylor (“Executive”) and Codexis, Inc.

February 27, 2023 EX-10.22B

Change in Control Severance Agreement by and between the Company and Margaret Fitzgerald dated October 10, 2022.

CODEXIS, INC. CHANGE OF CONTROL SEVERANCE AGREEMENT This Change of Control Severance Agreement (the “Agreement”) is made and entered into by and between Margaret Fitzgerald (the “Executive”) and Codexis, Inc., a Delaware corporation (the “Company”), effective as of the latest date set forth by the signatures of the parties hereto below (the “Effective Date”). R E C I T A L S A.It is expected that

February 27, 2023 EX-10.19A

Enzyme Supply Agreement by and between the Company and Pfizer Ireland Pharmaceuticals, dated as of July 14, 2022.

CONFIDENTIAL Certain information is this document, marked by brackets, has been omitted because it is both (i) not material and (ii) is the type that the registrant treats as private or confidential.

February 27, 2023 EX-10.22A

(incorporated by reference to Exhibit 10.13A to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Codexis, Inc. 200 Penobscot Drive Redwood City, CA 94063 Tel: +1 (650) 421-8100 Fax: +1 (650) 421-8102 www.codexis.com October 5, 2022 Margaret Fitzgerald Dear Margaret, On behalf of Codexis, Inc. (“Codexis” or the “Company”), I am pleased to extend to you this offer of employment as Chief Legal and Compliance Officer reporting to Stephen Dilly, President and CEO. Your position is a full-time and

February 27, 2023 EX-10.19C

Amendment No. 2 to the Enzyme Supply Agreement by and between the Company and Pfizer Ireland Pharmaceuticals, effective as of February 1, 2023.

AMENDMENT NO. 2 TO ENZYME SUPPLY AGREEMENT This Amendment No. 2 to Enzyme Supply Agreement (this “Amendment”) is made as of February 1, 2023 (the “Amendment Effective Date”), between Codexis, Inc., a Delaware corporation having its principal offices at 200 Penobscot Drive, Redwood City, California 94063 (“Codexis”) and Pfizer Ireland Pharmaceuticals, an Ireland corporation, with its principal plac

February 23, 2023 EX-99.1

Codexis Reports Fourth Quarter and Fiscal Year 2022 Financial Results Biotherapeutics Application of CodeEvolver® Validated by Recent Data Supporting the Potential for Three Upcoming Investigational New Drug Applications Cash Runway Through End of 20

Exhibit 99.1 Codexis Reports Fourth Quarter and Fiscal Year 2022 Financial Results Biotherapeutics Application of CodeEvolver® Validated by Recent Data Supporting the Potential for Three Upcoming Investigational New Drug Applications Cash Runway Through End of 2024 Funds Important Upcoming Milestones Company Provides 2023 Revenue Guidance REDWOOD CITY, Calif., February 23, 2023 (GLOBE NEWSWIRE) -

February 23, 2023 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): February 23, 2023 Codexis, Inc. (

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): February 23, 2023 Codexis, Inc. (Exact name of Registrant as Specified in its Charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 14, 2023 SC 13G/A

CDXS / Codexis, Inc. / Nantahala Capital Management, LLC - SC 13G/A Passive Investment

SC 13G/A 1 tm236168d21sc13ga.htm SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 10)* Codexis, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 192005106 (CUSIP Number) December 31, 2022 (Date of Event which Requires Filing of this Statement) Check th

February 14, 2023 SC 13G/A

CDXS / Codexis, Inc. / Casdin Capital, LLC Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No.

February 10, 2023 SC 13G/A

CDXS / Codexis, Inc. / ARK Investment Management LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No.

February 9, 2023 SC 13G/A

CDXS / Codexis, Inc. / VANGUARD GROUP INC - SCHEDULE 13G/A Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 1)* Name of issuer: Codexis Inc. Title of Class of Securities: Common Stock CUSIP Number: 192005106 Date of Event Which Requires Filing of this Statement: December 30, 2022 Check the appropriate box to designate the rule pursuant to which this Schedule is filed: ☒ Rule 1

February 3, 2023 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 3, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

January 23, 2023 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 23, 2023 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

January 9, 2023 EX-99.3

Form of Restricted Stock Unit Award Grant Notice and Restricted Stock Unit Award Agreement under the 2022 Employment Inducement Award Plan (incorporated by reference to Exhibit 99.3 to the Company's Registration Statement on Form S-8 (File No. 333-269163) filed with the SEC on January 9, 2023).

Exhibit 99.3 CODEXIS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN RESTRICTED STOCK UNIT AWARD GRANT NOTICE Codexis, Inc., a Delaware corporation (the “Company”), pursuant to its 2022 Employment Inducement Award Plan, as amended from time to time (the “Plan”), hereby grants to the individual listed below (“Participant”), an award of restricted stock units (“Restricted Stock Units” or “RSUs”). Each R

January 9, 2023 EX-99.2

Form of Stock Option Grant Notice and Stock Option Agreement under the 2022 Employment Inducement Award Plan (incorporated by reference to Exhibit 99.2 to the Company's Registration Statement on Form S-8 (File No. 333-269163) filed with the SEC on January 9, 2023).

Exhibit 99.2 CODEXIS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN STOCK OPTION GRANT NOTICE Codexis, Inc., a Delaware corporation, (the “Company”), pursuant to its 2022 Employment Inducement Award Plan, as amended from time to time (the “Plan”), hereby grants to the holder listed below (“Participant”), an option to purchase the number of shares of the Company’s common stock, par value $0.0001 (“Sto

January 9, 2023 S-8

As filed with the Securities and Exchange Commission on January 9, 2023

As filed with the Securities and Exchange Commission on January 9, 2023 Registration No.

January 9, 2023 EX-FILING FEES

Filing Fee Table

Exhibit 107.1 Calculation of Filing Fee Tables Form S-8 (Form Type) Codexis, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered (1) Proposed Maximum Offering Price Per Share (2) Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common Stock, $0.0001 par

January 9, 2023 EX-99.1

2022 Employment Inducement Award Plan

Exhibit 99.1 CODEXIS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN ARTICLE 1. PURPOSE The purpose of the Codexis, Inc. 2022 Employment Inducement Award Plan (as it may be amended or restated from time to time, the “Plan”) is to promote the success and enhance the value of Codexis, Inc. (the “Company”) by providing flexibility to the Company in its ability to motivate, attract, and retain the service

December 20, 2022 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 16, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

November 29, 2022 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 28, 2022 Codexis, Inc. (

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 28, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

November 4, 2022 EX-10.4

Change in Control Severance Agreement by and between the Company and Kevin Norrett dated September 12, 2022 (incorporated by reference to Exhibit 10.4 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2022, filed on November 4, 2022).

CODEXIS, INC. CHANGE OF CONTROL SEVERANCE AGREEMENT This Change of Control Severance Agreement (the “Agreement”) is made and entered into by and between Kevin Norrett (the “Executive”) and Codexis, Inc., a Delaware corporation (the “Company”), effective as of the latest date set forth by the signatures of the parties hereto below (the “Effective Date”). R E C I T A L S A.It is expected that the Co

November 4, 2022 EX-10.5

Enzyme Supply Agreement by and between the Company and Pfizer Ireland Pharmaceuticals,

CONFIDENTIAL Certain information is this document, marked by brackets, has been omitted because it is both (i) not material and (ii) is the type that the registrant treats as private or confidential.

November 4, 2022 EX-10.1

Transition and Separation Agreement by and between the Company and John Nicols, dated as of July 18, 2022 (incorporated by reference to Exhibit 10.1 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2022, filed on November 4, 2022).

EXECUTION COPY TRANSITION AND SEPARATION AGREEMENT This Transition and Separation Agreement (the “Agreement”) by and between John Nicols (“Executive”) and Codexis, Inc.

November 4, 2022 EX-10.2

Employment Agreement by and between the Company and Stephen Dilly dated as of August 9, 2022 (incorporated by reference to Exhibit 10.2 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2022, filed on November 4, 2022).

Employment Agreement This Employment Agreement (the “Agreement”), dated as of August 9, 2022 (the “Effective Date”), is made by and between Codexis, Inc.

November 4, 2022 EX-10.3

Offer Letter by and between the Company and Kevin Norrett dated as of September 12, 2022 (incorporated by reference to Exhibit 10.3 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2022, filed on November 4, 2022).

Codexis, Inc. 200 Penobscot Drive Redwood City, CA 94063 Tel: +1 (650) 421-8100 Fax: +1 (650) 421-8102 www.codexis.com September 12, 2022 Kevin Norrett Dear Kevin, On behalf of Codexis, Inc. (“Codexis” or the “Company”), I am pleased to extend to you this offer of employment as Chief Operating Officer reporting to Stephen Dilly, President and CEO. Your position is a full-time and exempt from overt

November 4, 2022 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2022 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codex

November 3, 2022 EX-99.1

Codexis Reports Third Quarter 2022 Financial Results Reiterates 2022 Total Revenue Guidance of $135M-$141M, Including Product Revenues of $112M-$118M

Exhibit 99.1 Codexis Reports Third Quarter 2022 Financial Results Reiterates 2022 Total Revenue Guidance of $135M-$141M, Including Product Revenues of $112M-$118M REDWOOD CITY, Calif., November 3, 2022 - Codexis, Inc. (NASDAQ: CDXS), a leading enzyme engineering company enabling the promise of synthetic biology, today announced financial results for the third quarter ended September 30, 2022 and p

November 3, 2022 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 3, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

October 3, 2022 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 8, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

August 5, 2022 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2022 or ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis, I

August 5, 2022 EX-10.1

Platform Technology Transfer, Collaboration and License Agreement by and between the Company and GlaxoSmithKline Intellectual Property Limited, effective as of July 10, 2014.

EXECUTION COPY PLATFORM TECHNOLOGY TRANSFER, COLLABORATION AND LICENSE AGREEMENT BY AND BETWEEN CODEXIS, INC.

August 4, 2022 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 4, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numbe

August 4, 2022 EX-99.1

Codexis Reports Second Quarter 2022 Financial Results Total Revenue up 51% and Product Revenue up 135% YOY 2022 Total Revenue Guidance of $135M-$141M, Including Product Revenues of $112M-$118M

Exhibit 99.1 Codexis Reports Second Quarter 2022 Financial Results Total Revenue up 51% and Product Revenue up 135% YOY 2022 Total Revenue Guidance of $135M-$141M, Including Product Revenues of $112M-$118M REDWOOD CITY Calif., August 4, 2022 - Codexis, Inc. (NASDAQ: CDXS), a leading enzyme engineering company enabling the promise of synthetic biology, today announced financial results for the seco

July 18, 2022 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 17, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

July 14, 2022 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 14, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

July 14, 2022 EX-99.1

Codexis Announces Preliminary Second Quarter 2022 Results and Updates Guidance Final financial results for the second quarter to be reported on August 4, 2022

Exhibit 99.1 Codexis Announces Preliminary Second Quarter 2022 Results and Updates Guidance Final financial results for the second quarter to be reported on August 4, 2022 REDWOOD CITY, Calif., July 14, 2022 ? Codexis, Inc. (NASDAQ: CDXS), a leading enzyme engineering company enabling the promise of synthetic biology, today announced preliminary revenue results for the second quarter ending June 3

July 14, 2022 8-K

Entry into a Material Definitive Agreement

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 14, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

June 16, 2022 8-K

Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 14, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

May 9, 2022 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2022 or ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis,

May 5, 2022 EX-99.1

Codexis Reports First Quarter 2022 Financial Results Total Revenue up 96% and Product Revenue up 200% YOY; Product Gross Margin Expands to 72% Reiterating Guidance for 2022, Including Total Revenue of $152 - $158M

Exhibit 99.1 Codexis Reports First Quarter 2022 Financial Results Total Revenue up 96% and Product Revenue up 200% YOY; Product Gross Margin Expands to 72% Reiterating Guidance for 2022, Including Total Revenue of $152 - $158M REDWOOD CITY Calif., May 5, 2022 ? Codexis, Inc. (Nasdaq: CDXS), a leading enzyme engineering company enabling the promise of synthetic biology, today announced financial re

May 5, 2022 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 5, 2022 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number)

April 28, 2022 DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ? Filed by a party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ? Definitive Proxy State

April 28, 2022 DEF 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

DEF 14A 1 d335748ddef14a.htm DEF 14A Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as

February 28, 2022 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ? ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended: December 31, 2021 ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission File No.: 001-34705 Codexis, Inc. (Ex

February 28, 2022 EX-10.13A

Platform Technology Transfer and License Agreement by and between the Company and Merck Sharp & Dohme Corp., dated as of August 3, 2015

[***] Certain information in this document, indicated by brackets, has been excluded pursuant to Regulation S-K, Item 601(b)(10)(iv).

February 28, 2022 EX-4.3

Description of the Common Stock of Codexis, Inc. (incorporated by reference to Exhibit 4.3 to the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2021, filed on February 28, 2022).

Exhibit 4.3 DESCRIPTION OF THE REGISTRANT?S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 As of February 28, 2022, Codexis, Inc. (?we,? ?us? or ?our?) had one class of securities registered under Section 12 of the Securities Exchange Act of 1934, as amended: our common stock, $0.0001 par value per share (?common stock?). Description of Common Stock The followi

February 24, 2022 8-K

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): February 24, 2022 Codexis, Inc. (Exact name of Registrant as Specified in its Charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 24, 2022 EX-99.2

Q4 & FY’2021 Results February 24, 2022 We engineer enzymes to improve health… of people and the planet • These slides and any accompanying oral presentation contain forward-looking statements that involve risks and uncertainties. These statements rel

Q4 & FY?2021 Results February 24, 2022 We engineer enzymes to improve health? of people and the planet ? These slides and any accompanying oral presentation contain forward-looking statements that involve risks and uncertainties.

February 24, 2022 EX-99.1

Codexis Reports Fourth Quarter and Fiscal Year 2021 Financial Results Record Annual Total Revenue of $104.8M, Representing Eighth Consecutive Year of Revenue Growth Company Guides to 2022 Total Revenues of $152-$158M; Product Revenues of $112-$118M

Exhibit 99.1 Codexis Reports Fourth Quarter and Fiscal Year 2021 Financial Results Record Annual Total Revenue of $104.8M, Representing Eighth Consecutive Year of Revenue Growth Company Guides to 2022 Total Revenues of $152-$158M; Product Revenues of $112-$118M REDWOOD CITY Calif., February 24, 2022 ? Codexis, Inc. (Nasdaq:CDXS), a leading enzyme engineering company enabling the promise of synthet

February 10, 2022 SC 13G/A

CDXS / Codexis, Inc. / Nantahala Capital Management, LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 9)* Codexis, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 192005106 (CUSIP Number) January 31, 2022 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the rule purs

February 9, 2022 SC 13G

CDXS / Codexis, Inc. / VANGUARD GROUP INC - SCHEDULE 13G Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 Name of issuer: Codexis Inc. Title of Class of Securities: Common Stock CUSIP Number: 192005106 Date of Event Which Requires Filing of this Statement: December 31, 2021 Check the appropriate box to designate the rule pursuant to which this Schedule is filed: ☒ Rule 13d-1(b) ☐ Rule 13d-1

February 9, 2022 SC 13G/A

CDXS / Codexis, Inc. / ARK Investment Management LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No.

January 10, 2022 SC 13G/A

CDXS / Codexis, Inc. / ARK Investment Management LLC - SCHEDULE 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No.

November 5, 2021 EX-10.1

, by and between the Company and Merck Sharp and Dohme Corp. (incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 20

[***] Certain information in this document has been excluded pursuant to Regulation S-K, Item 601(b)(10).

November 5, 2021 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2021 or ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codex

November 5, 2021 EX-10.2

Ninth Amendment to Loan and Security Agreement by and between the Company and Western Alliance Bank dated as of September 30, 2021 (incorporated by reference to Exhibit 10.2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2021, filed on November 5, 2021

Exhibit 10.2 NINTH AMENDMENT TO LOAN AND SECURITY AGREEMENT THIS NINTH AMENDMENT to Loan and Security Agreement (this ?Amendment?) is made effective as of September 30, 2021 (the ?Amendment Date?) and made by and among WESTERN ALLIANCE BANK, an Arizona corporation (?Bank?) and CODEXIS, INC., a Delaware corporation (?Borrower?). WHEREAS, Bank and Borrower have entered into that certain Loan and Sec

November 4, 2021 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 4, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

November 4, 2021 EX-99.1

Codexis Reports Third Quarter 2021 Financial Results Record Quarterly Total Revenue, Product Revenue and Product Gross Margin Reiterating Total Revenue Guidance of $98-103M; Raising Product Revenue Guidance to $63-66M

Exhibit 99.1 Codexis Reports Third Quarter 2021 Financial Results Record Quarterly Total Revenue, Product Revenue and Product Gross Margin Reiterating Total Revenue Guidance of $98-103M; Raising Product Revenue Guidance to $63-66M REDWOOD CITY Calif., November 4, 2021 ? Codexis, Inc. (Nasdaq:CDXS), a leading enzyme engineering company enabling the promise of synthetic biology, today announced fina

October 14, 2021 8-K

Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 14, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

September 9, 2021 8-K

Regulation FD Disclosure, Entry into a Material Definitive Agreement, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 9, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

September 9, 2021 EX-99.1

Codexis and Merck Amend and Extend Supply Agreement for Enzyme Used in Manufacture of Sitagliptin

Exhibit 99.1 Codexis and Merck Amend and Extend Supply Agreement for Enzyme Used in Manufacture of Sitagliptin REDWOOD CITY, Calif., September 9, 2021 - Codexis, Inc. (Nasdaq: CDXS), a leading enzyme engineering company enabling the promise of synthetic biology, announced the amendment and extension of its agreement with Merck, known as MSD outside the United States and Canada, to license and supp

August 25, 2021 8-K

Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 25, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numb

August 6, 2021 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2021 or ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis, I

August 5, 2021 EX-99.1

Codexis Reports Second Quarter 2021 Financial Results Record Product Revenue of $14.7M, up 227% YOY Record Product Gross Margin of 71% Company Raises Guidance for 2021 Total Revenue to $98 - 103 M and 2021 Product Revenue to $59 - 63 M

Exhibit 99.1 Codexis Reports Second Quarter 2021 Financial Results Record Product Revenue of $14.7M, up 227% YOY Record Product Gross Margin of 71% Company Raises Guidance for 2021 Total Revenue to $98 - 103 M and 2021 Product Revenue to $59 - 63 M REDWOOD CITY Calif., August 5, 2021 ? Codexis, Inc. (Nasdaq:CDXS), a leading enzyme engineering company enabling the promise of synthetic biology, toda

August 5, 2021 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 5, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numbe

July 9, 2021 SC 13G/A

CDXS / Codexis, Inc. / ARK Investment Management LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No.

June 17, 2021 8-K

Other Events, Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 15, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

June 17, 2021 8-K

Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 17, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

May 7, 2021 S-3ASR

- S-3ASR

Table of Contents As filed with the Securities and Exchange Commission on May 7, 2021 Registration No.

May 7, 2021 EX-10.1

Lease Agreement by and between the Company and ARE-SAN FRANCISCO NO. 63, LLC dated as of January 29, 2021 (incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2021, filed on May 7, 2021).

[***] Certain information in this document has been excluded pursuant to Regulation S-K, Item 601(b)(10).

May 7, 2021 424B5

The date of this prospectus supplement is May 7, 2021

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-255926 PROSPECTUS SUPPLEMENT (To prospectus dated May 7, 2021) Up to $50,000,000 Common Stock We have entered into an Equity Distribution Agreement, or the Equity Distribution Agreement, with Piper Sandler & Co., or Piper Sandler, relating to shares of our common stock offered by this prospectus supplement and the accomp

May 7, 2021 EX-1.1

Equity Distribution Agreement, dated as of May 7, 2021, between Codexis, Inc. and Piper Sandler & Co. (incorporated by reference to Exhibit 1.1 to the Company’s Current Report on Form 8-K, filed on May 5, 2021).

Exhibit 1.1 CODEXIS, INC. EQUITY DISTRIBUTION AGREEMENT May 7, 2021 PIPER SANDLER & CO. U.S. Bancorp Center 800 Nicollet Mall Minneapolis, Minnesota 55402 Ladies and Gentlemen: As further set forth in this agreement (this ?Agreement?), Codexis, Inc., a company organized under the laws of Delaware (the ?Company?), proposes to issue and sell from time to time through Piper Sandler & Co. (the ?Agent?

May 7, 2021 EX-4.7

Form of Indenture (incorporated by reference to Exhibit 4.7 to the Company’s Registration Statement on Form S-3, filed on May 7, 2021).

Exhibit 4.7 CODEXIS, INC. INDENTURE Dated as of , 20 [ ], Trustee TABLE OF CONTENTS Page ARTICLE I. DEFINITIONS AND INCORPORATION BY REFERENCE 1 Section 1.1. Definitions 1 Section 1.2. Other Definitions 4 Section 1.3. Incorporation by Reference of Trust Indenture Act 4 Section 1.4. Rules of Construction 5 ARTICLE II. THE SECURITIES 5 Section 2.1. Issuable in Series 5 Section 2.2. Establishment of

May 7, 2021 10-Q

Quarterly Report - 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2021 or ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis,

May 7, 2021 8-K

Entry into a Material Definitive Agreement, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 7, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number)

May 6, 2021 EX-99.1

Codexis Reports First Quarter 2021 Financial Results Total Revenue up 23% and Product Revenue Doubles Year over Year

Exhibit 99.1 Codexis Reports First Quarter 2021 Financial Results Total Revenue up 23% and Product Revenue Doubles Year over Year REDWOOD CITY Calif., May 6, 2021 ? Codexis, Inc. (Nasdaq:CDXS), a leading enzyme engineering company enabling the promise of synthetic biology, today announced financial results for the first quarter ended March 31, 2021 and provided a business update. ?Codexis? growth

May 6, 2021 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 6, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number)

April 29, 2021 DEFA14A

- DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ? Filed by a party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ? Definitive Proxy State

April 29, 2021 DEF 14A

- DEF 14A

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ? Filed by a party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ? Defi

March 1, 2021 10-K

Annual Report - 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ? ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended: December 31, 2020 ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission File No.: 001-34705 Codexis, Inc. (Ex

February 25, 2021 EX-99.2

Q4 & FY’2020 Results February 25, 2021 We engineer enzymes to improve health… of people and the planet • These slides and any accompanying oral presentation contain forward-looking statements that involve risks and uncertainties. These statements rel

Q4 & FY?2020 Results February 25, 2021 We engineer enzymes to improve health? of people and the planet ? These slides and any accompanying oral presentation contain forward-looking statements that involve risks and uncertainties.

February 25, 2021 EX-99.1

Codexis Reports Fourth Quarter and Fiscal Year 2020 Financial Results Strong Product Revenue Momentum in Second Half of 2020 Drives Company’s Seventh Consecutive Year of YOY Revenue Growth Full Year Product Gross Margin Exceeds 50% for the First Time

Exhibit 99.1 Codexis Reports Fourth Quarter and Fiscal Year 2020 Financial Results Strong Product Revenue Momentum in Second Half of 2020 Drives Company’s Seventh Consecutive Year of YOY Revenue Growth Full Year Product Gross Margin Exceeds 50% for the First Time in Company’s History Company Guides to 2021 Total Revenues of $82-85M, Product Revenues of $36-39M REDWOOD CITY Calif., February 25, 202

February 25, 2021 8-K

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): February 25, 2021 Codexis, Inc. (Exact name of Registrant as Specified in its Charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 18, 2021 8-K/A

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K/A CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 3, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File N

February 16, 2021 SC 13D

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Exchange Act of 1934 (Amendment No. )* Codexis, Inc. (Name of Issuer) Common Stock, par value $0.0001 value per share (Title of Class of Securit

SC 13D UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Exchange Act of 1934 (Amendment No. )* Codexis, Inc. (Name of Issuer) Common Stock, par value $0.0001 value per share (Title of Class of Securities) 192005106 (CUSIP Number) John Nicols c/o Codexis, Inc. 200 Penobscot Drive Redwood City, CA 94063 (Name, Address and Telephone Number of P

February 16, 2021 SC 13G/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 8)* Codexis, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 8)* Codexis, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 192005106 (CUSIP Number) December 31, 2020 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pur

February 16, 2021 SC 13G

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. )* Codexis, Inc. (Name of Issuer) Common stock (Title of Class of Securities) (CUSIP Number) December 31, 2020

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No.

February 12, 2021 EX-99.1

Joint Filing Agreement

Exhibit 99.1 Joint Filing Agreement The undersigned hereby agree that the Statement on the Schedule 13G filed herewith (and any amendments thereto), relating to the common stock of Codexis, Inc. is being filed jointly with the Securities and Exchange Commission pursuant to Rule 13d-1(c) under the Securities Exchange Act of 1934, as amended, on behalf of each of the undersigned. This Agreement may

February 12, 2021 SC 13G/A

SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G* (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2 (AMENDMENT NO. 3)*

SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G* (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2 (AMENDMENT NO. 3)* Codexis, Inc. (Name of Issuer) Common stock, par value $0.0001 per share (Title of Class of Securities) 192005106 (CUSIP Number) December 31, 2020 (Date o

February 11, 2021 SC 13G/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)*

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No.

February 9, 2021 8-K

Entry into a Material Definitive Agreement - 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 8, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

February 3, 2021 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers - 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 3, 2021 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

December 7, 2020 EX-1.1

Underwriting Agreement, dated as of December 2, 2020, among Codexis, Inc. and Jefferies LLC, Cowen and Company, LLC and Stifel, Nicolaus & Company, Incorporated, as representatives of the underwriters named therein.

EX-1.1 Exhibit 1.1 Execution Version 4,285,715 Shares Codexis, Inc. UNDERWRITING AGREEMENT December 2, 2020 JEFFERIES LLC COWEN AND COMPANY, LLC STIFEL, NICOLAUS & COMPANY, INCORPORATED As Representatives of the several Underwriters c/o JEFFERIES LLC 520 Madison Avenue New York, New York 10022 c/o COWEN AND COMPANY, LLC 599 Lexington Avenue New York, NY 10022 c/o STIFEL, NICOLAUS & COMPANY, INCORP

December 7, 2020 8-K

Financial Statements and Exhibits, Other Events - 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 2, 2020 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

December 3, 2020 424B5

CALCULATION OF REGISTRATION FEE TITLE OF EACH CLASS OF SECURITIES TO BE REGISTERED AMOUNT TO BE REGISTERED(1) PROPOSED MAXIMUM OFFERING PRICE PER SHARE PROPOSED MAXIMUM AGGREGATE OFFERING PRICE AMOUNT OF REGISTRATION FEE(2) Common stock, par value $0

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-228693 CALCULATION OF REGISTRATION FEE TITLE OF EACH CLASS OF SECURITIES TO BE REGISTERED AMOUNT TO BE REGISTERED(1) PROPOSED MAXIMUM OFFERING PRICE PER SHARE PROPOSED MAXIMUM AGGREGATE OFFERING PRICE AMOUNT OF REGISTRATION FEE(2) Common stock, par value $0.0001 per share 4,928,572 $17.50 $86,250,010.00 9,410 (1) Include

December 2, 2020 424B5

Shares Codexis, Inc. Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-228693 The information contained in this preliminary prospectus supplement and the accompanying prospectus is not complete and may be changed. A registration statement relating to the securities has been declared effective by the Securities and Exchange Commission. This preliminary prospectus supplement and the accompanying pr

November 24, 2020 8-K/A

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers - 8-K/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K/A CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 5, 2020 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

November 6, 2020 10-Q

Quarterly Report - 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2020 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codex

November 6, 2020 EX-10.1

Eighth Amendment to Loan and Security Agreement by and between the Company and Western Alliance Bank dated as of September 30, 2020 (incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2020, filed on November 6, 2020.)

Exhibit 10.1 EIGHTH AMENDMENT TO LOAN AND SECURITY AGREEMENT THIS EIGHTH AMENDMENT to Loan and Security Agreement (this “Amendment”) is made effective as of September 30, 2020 (the “Amendment Date”) and made by and among WESTERN ALLIANCE BANK, an Arizona corporation (“Bank”) and CODEXIS, INC., a Delaware corporation (“Borrower”). WHEREAS, Bank and Borrower have entered into that certain Loan and S

November 5, 2020 EX-99.1

Codexis Reports Third Quarter 2020 Financial Results Stronger than expected total revenues of $18.4 million delivered in the quarter Higher sequential sales expected again in the fourth quarter, showing growing momentum as we close 2020 Conference ca

Exhibit 99.1 Codexis Reports Third Quarter 2020 Financial Results Stronger than expected total revenues of $18.4 million delivered in the quarter Higher sequential sales expected again in the fourth quarter, showing growing momentum as we close 2020 Conference call begins at 4:30 p.m. Eastern time today REDWOOD CITY, Calif. (November 5, 2020) – Codexis, Inc. (Nasdaq: CDXS), a leading protein engin

November 5, 2020 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition - 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 5, 2020 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

August 10, 2020 10-Q

Quarterly Report - 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2020 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis, I

August 6, 2020 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 5, 2020 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numbe

August 6, 2020 EX-99.1

Codexis Reports Second Quarter 2020 Financial Results Revenues increased 21% to $15 million; 72% rise in R&D revenue included a significant contribution from the Takeda biotherapeutics partnership Conference call with slides begins at 4:30 p.m. Easte

Exhibit 99.1 Codexis Reports Second Quarter 2020 Financial Results Revenues increased 21% to $15 million; 72% rise in R&D revenue included a significant contribution from the Takeda biotherapeutics partnership Conference call with slides begins at 4:30 p.m. Eastern time today REDWOOD CITY, Calif. (August 6, 2020) - Codexis, Inc. (Nasdaq: CDXS), a leading protein engineering company, announces fina

June 22, 2020 8-K

Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 16, 2020 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number

May 28, 2020 DEFA14A

- DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy State

May 8, 2020 EX-10.1

Strategic Collaboration and License Agreement by and between Shire Human Genetic Therapies, Inc., a wholly-owned subsidiary of Takeda Pharmaceutical Company Limited and the Company, dated March 23, 2020 (incorporated by reference to Exhibit 10.1 to the Company's Quarterly Report on Form 10-Q for the quarter ended March 31, 2020, filed on May 8, 2020)

Exhibit 10.1 [***] Certain information in this document has been excluded pursuant to Regulation S-K, Item 601(b)(10). Such excluded information is not material and would likely cause competitive harm to the registration if publicly disclosed. STRATEGIC COLLABORATION AND LICENSE AGREEMENT This Strategic Collaboration and License Agreement (this “Agreement”) is made as of March 23, 2020 (the “Effec

May 8, 2020 EX-10.2

Letter Agreement, effective as of February 21, 2020, by and between Codexis, Inc. and GlaxoSmithKline Intellectual Property Development Limited (incorporated by reference to Exhibit 10.2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2020, filed on May 8, 2020).

Exhibit 10.2 [***] Certain information in this document has been excluded pursuant to Regulation S-K, Item 601(b)(10). Such excluded information is not material and would likely cause competitive harm to the registration if publicly disclosed. GlaxoSmithKline Intellectual Property Development Limited Letterhead 7th February 2020 Codexis, Inc. 200 Penobscot Drive Redwood City, CA 94063 Telephone: [

May 8, 2020 10-Q

Quarterly Report - 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2020 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codexis,

May 7, 2020 EX-99.1

Codexis Reports First Quarter 2020 Financial Results R&D revenue increased 26% to $9.6 million fueled by the Novartis and Takeda strategic collaborations Withdraws 2020 financial guidance due to uncertainty of COVID-19 potential impact Conference cal

Exhibit 99.1 Codexis Reports First Quarter 2020 Financial Results R&D revenue increased 26% to $9.6 million fueled by the Novartis and Takeda strategic collaborations Withdraws 2020 financial guidance due to uncertainty of COVID-19 potential impact Conference call begins at 4:30 pm Eastern time today REDWOOD CITY, Calif. (May 7, 2020) - Codexis, Inc. (Nasdaq: CDXS), a leading protein engineering c

May 7, 2020 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 7, 2020 Codexis, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Number)

April 28, 2020 DEFA14A

- DEFA14A

DEFA14A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Pro

April 28, 2020 DEF 14A

definitive proxy statement

DEF 14A Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.

March 23, 2020 8-K

Regulation FD Disclosure, Entry into a Material Definitive Agreement, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): March 19, 2020 Codexis, Inc. (Exact name of Registrant as Specified in its Charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Numbe

February 28, 2020 10-K

Annual Report - 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended: December 31, 2019 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . Commission File No.: 001-34705 Codexis, Inc. (Ex

February 28, 2020 EX-21.1

List of Subsidiaries.

Exhibit 21.1 Subsidiaries of Codexis, Inc. None. 1 1 In accordance with Item 601(b)(21)(ii) of Regulation S-K, the registrant has omitted from this exhibit the names of its subsidiaries which, considered in the aggregate or as a single subsidiary, do not constitute a significant subsidiary as defined in Rule 1-02(w) of Regulation S-X.

February 28, 2020 EX-4.3

Description of the Common Stock of Codexis, In

Exhibit 4.3 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 As of December 31, 2019, Codexis, Inc. (“we,” “us” or “our”) had one class of securities registered under Section 12 of the Securities Exchange Act of 1934, as amended: our common stock, $0.0001 par value per share (“common stock”). Description of Common Stock The followi

February 27, 2020 EX-99.1

Codexis Reports 2019 Fourth Quarter and Full Year Financial Results 2019 total revenues increased 13% to $68.5 million with product revenue up 15% and R&D revenue up 11% Ten customers contributed more than $1 million each to 2019 revenues Introduces

Exhibit 99.1 Codexis Reports 2019 Fourth Quarter and Full Year Financial Results 2019 total revenues increased 13% to $68.5 million with product revenue up 15% and R&D revenue up 11% Ten customers contributed more than $1 million each to 2019 revenues Introduces 2020 financial guidance Conference call with slides begins at 4:30 pm Eastern time today REDWOOD CITY, Calif. (February 27, 2020) – Codex

February 27, 2020 8-K

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): February 27, 2020 Codexis, Inc. (Exact name of Registrant as Specified in its Charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Nu

February 27, 2020 EX-99.2

Unlock the power of proteins TM February 27, 2020 Investor Call 4Q’19 and FY’19 Results; 2020 Guidance and Outlook Nasdaq: CDXS Forward-Looking Statements • These slides and the accompanying oral presentation contain forward-looking statements that i

codexisinvestorcallfeb27 Unlock the power of proteins TM February 27, 2020 Investor Call 4Q’19 and FY’19 Results; 2020 Guidance and Outlook Nasdaq: CDXS Forward-Looking Statements • These slides and the accompanying oral presentation contain forward-looking statements that involve risks and uncertainties.

February 12, 2020 SC 13G/A

CDXS / Codexis, Inc. / Nantahala Capital Management, LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 7)* Codexis, Inc. (Name of Issuer) Common Stock, par value $0.0001 per share (Title of Class of Securities) 192005106 (CUSIP Number) December 31, 2019 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pur

November 6, 2019 8-K

Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of report (Date of earliest event reported): November 6, 2019 Codexis, Inc. (Exact name of Registrant as Specified in its Charter) Delaware 001-34705 71-0872999 (State or other jurisdiction of incorporation) (Commission File Num

November 6, 2019 424B7

CALCULATION OF REGISTRATION FEE Title of Each Class of Securities to be Registered Amount to be Registered(1) Proposed Maximum Offering Price Per Share Proposed Maximum Aggregate Offering Price Amount of Registration Fee(2) Common Stock, par value $0

424B7 Filed Pursuant to Rule 424(b)(7) Registration No. 333-228693 CALCULATION OF REGISTRATION FEE Title of Each Class of Securities to be Registered Amount to be Registered(1) Proposed Maximum Offering Price Per Share Proposed Maximum Aggregate Offering Price Amount of Registration Fee(2) Common Stock, par value $0.0001 3,048,780 $13.46 (3) $41,036,579 $5,327 (1) Pursuant to Rule 416 under the Se

November 6, 2019 EX-10.1A

Sixth Amendment to Loan and Security Agreement by and between the Company and Western Alliance Bank dated as of July 11, 2019 (incorporated by reference to Exhibit 10.1A to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2019, filed on November 6, 2019).

Exhibit 10.1A SIXTH AMENDMENT TO LOAN AND SECURITY AGREEMENT THIS SIXTH AMENDMENT to Loan and Security Agreement (this “Amendment”) is made effective as of July 11, 2019 (the “Amendment Date”) and made by and among WESTERN ALLIANCE BANK, an Arizona corporation (“Bank”) and CODEXIS, INC., a Delaware corporation (“Borrower”). WHEREAS, Bank and Borrower have entered into that certain Loan and Securit

November 6, 2019 10-Q

Quarterly Report - 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2019 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-34705 Codex

November 6, 2019 EX-10.3

(incorporated by reference to Exhibit 10.3 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2019, filed

Codexis, Inc. 200 Penobscot Drive Redwood City, CA 94063 Tel: +1 (650) 421-8100 Fax: +1 (650) 421-8102 www.codexis.com Exhibit 10.3 August 4, 2019 Ross Taylor Via email: ############@###.## Dear Ross: On behalf of Codexis, I am pleased to extend to you this offer of employment as Senior Vice President, Chief Financial Officer reporting to John Nicols, President & CEO. Your position is a full-time

November 6, 2019 EX-10.2

Form of Amended and Restated Change in Control Severance Agreement between the Company and certain of its officers (incorporated by reference to Exhibit 10.2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2019, filed on November 6, 2019).

Exhibit 10.2 CODEXIS, INC. CHANGE OF CONTROL SEVERANCE AGREEMENT This Change of Control Severance Agreement (the “Agreement”) is made and entered into by and between (the “Executive”) and Codexis, Inc., a Delaware corporation (the “Company”), effective as of the latest date set forth by the signatures of the parties hereto below (the “Effective Date”). R E C I T A L S A.It is expected that the Com

November 6, 2019 EX-10.1B

Seventh Amendment to Loan and Security Agreement by and between the Company and Western Alliance Bank dated as of September 30, 2019 (incorporated by reference to Exhibit 10.1B to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2019, filed on November 6, 2019).

Exhibit 10.1B SEVENTH AMENDMENT TO LOAN AND SECURITY AGREEMENT THIS SEVENTH AMENDMENT to Loan and Security Agreement (this “Amendment”) is made effective as of September 30, 2019 (the “Amendment Date”) and made by and among WESTERN ALLIANCE BANK, an Arizona corporation (“Bank”) and CODEXIS, INC., a Delaware corporation (“Borrower”). WHEREAS, Bank and Borrower have entered into that certain Loan an

November 6, 2019 EX-10.4

Amendment to Employment Agreement between the Company and John Nicols, effective as of June 28, 2019 (incorporated by reference to Exhibit 10.4 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2019, filed on November 6, 2019).

Exhibit 10.4 June 28, 2019 John Nicols 200 Penobscot Drive Redwood City, CA 94063 Re: Amendment to Employment Agreement Dear John, You and Codexis, Inc. (the “Company”) are currently parties to an Employment Agreement, dated as of May 28, 2012, as amended on April 21, 2016 and November 16, 2017 (the “Employment Agreement”), which sets forth the terms of your employment with the Company and provide

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