What changed in this filing

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Item 9A. Controls and Procedures

2026-03-11 compared with 2025-02-27 · 66 added, 87 removed, 124 unchanged (55% of the section changed)

19 unchanged sentences

Rule 10b5-1 Trading Arrangements

During the three months ended December 31, 2024, none of the directors or executive officers of the Company adopted or terminated any contracts, instructions, or written plans for the purchase or sale of our securities that were intended to meet the affirmative defense conditions of Rule 10b5-1(c) or any other “non-Rule 10b5-1 trading arrangement.”

On September 15, 2025 , Stefan Lutz , Ph.D., who previously served as our Senior Vice President, Research and who became our Chief Technology Officer effective November 2025, adopted a trading plan intended to satisfy the affirmative defense conditions of Rule 10b5‑1(c).

The plan provides for the potential sale of up to 39,750 shares of the Company’s common stock and will terminate on October 16, 2026 , subject to early termination for certain specified events set forth in the plan.

Lutz became an officer of the Company (as defined in Rule 16a-1(f) of the Securities Exchange Act of 1934, as amended) during the three months ended December 31, 2025.

During the three months ended December 31, 2025, none of the directors or officers (as defined in Rule 16a-1(f) of the Securities Exchange Act of 1934, as amended) of the Company adopted or terminated any contracts, instructions, or written plans for the purchase or sale of our securities that were intended to meet the affirmative defense conditions of Rule 10b5-1(c) or any other “non-Rule 10b5-1 trading arrangement.”

DISCLOSURE REGARDING FOREIGN JURISDICTIONS THAT PREVENT INSPECTIONS

3 unchanged sentences

A copy of our code of ethics is available on our principal corporate website at www.codexis.com in the Investors section under “Corporate Governance.”

We intend to satisfy the disclosure requirement under Item 5.05 of Form 8-K regarding an amendment to, or waiver from, a provision of our code of ethics by posting such information on our website, at the address and location specified above and, to the extent required by the listing standards of the Nasdaq Global Select Market, by filing a Current Report on Form 8-K with the SEC, disclosing such information.

We have adopted insider trading policies and procedures governing the purchase, sale, and other dispositions of our securities by directors, officers and employees that are designed to promote compliance with insider trading laws, rules and regulations and applicable Nasdaq listing standards, as well as procedures designed to further the foregoing purposes.

A copy of our insider trading policy was filed as Exhibit 19.1 to our Annual Report on Form 10-K for the year ended December 31, 2024, which is incorporated herein by reference.

The information required by this item is incorporated by reference from the information that will be set forth in the 2026 Proxy Statement.

The Company has adopted an insider trading policy which governs transactions in our securities by the Company and its directors, officers, employees, and consultants, and is reasonably designed to promote compliance with insider trading laws, rules and regulations, as well as listing standards, applicable to the Company.

A copy of our insider trading policy is filed with this Annual Report on Form 10-K as Exhibit 19.1.

EXECUTIVE COMPENSATION

12 unchanged sentences

EXHIBIT INDEX

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 7, 2021).

3.1 Amended and Restated Certificate of Incorporation of Codexis, Inc.

2 unchanged sentences

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).

3.4 Second A mended and Restated Bylaws of Codexis, Inc.

3.4 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).

3 unchanged sentences

(incorporated by reference to Exhibit 4.1 to the Company’s Current Report on Form 8-K, filed on February 13, 2024).

Description of Codexis' Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934 (incorporated by reference to Exhibit 4.

4 to the Company’s Annual Report on Form 10-K for the year ended December 31, 202 3 , filed on February 28, 202 4 ).

10.1A* Lease Agreement by and between the Company and Metropolitan Life Insurance Company comm e ncing as of February 1, 2004.

Description of Codexis' Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934 (incorporated by reference to Exhibit 4.4 to the Company’s Annual Report on Form 10-K for the year ended December 31, 2023, filed on February 28, 2024).

10.1A* Lease Agreement by and between the Company and Metropolitan Life Insurance Company commencing as of February 1, 2004.

10.1B* Amendment to Lease Agreement by and between the Company and Metropolitan Life Insurance Company dated as of June 1, 2004.

6 unchanged sentences

Eighth Amendment to Lease, dated as of February 8, 2019, by and between the Company and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.3 to the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2019, filed on May 8, 2019).

10.1J*** Ninth Amendment to Lease, dated as of December 4, 202 4 , by and between the Company and Metropolitan Life Insurance Company.

10.2+* Codexis, Inc.

2010 Equity Incentive Award Plan and Form of Stock Option Agreement.

10.1J*** Ninth Amendment to Lease, dated as of December 4, 2024, by and between the Company and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.1J to the Company’s Annual Report Form 10-K for the year ended December 31, 2024, filed on February 27, 2025)

10.2A+ Codexis, Inc.

11 unchanged sentences

333-232262) filed with the SEC on June 21, 2019).

Amendment to the Codexis, Inc.

10.2G+ Amendment to the Codexis, Inc.

2019 Incentive Award Plan (incorporated by reference to Exhibit 10.2 to the Company’s Current Report on Form 8-K, filed on June 16, 2023).

Codexis, Inc.

10.2H+ Second Amendment to the Codexis, Inc.

2019 Incentive Award Plan, as amended (incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2025, filed on August 13, 2025).

10.3A+ Codexis, Inc.

2022 Employment Inducement Award Plan (incorporated by reference to Exhibit 99.1 to the Company's Registration Statement on Form S-8 (File No.

333-269163) filed with the SEC on January 9, 2023).

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.

10.3B+ 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).

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.

10.3C+ 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).

Codexis, Inc.

10.4A+ Codexis, Inc.

2023 Employee Stock Purchase Plan (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K, filed on June 16, 2023).

Amendment to the Codexis, Inc.

10.4B Amendment to the Codexis, Inc.

2023 Employee Stock Purchase Plan.

2 unchanged sentences

10.6+ 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).

Asset Purchase Agreement, dated October 28, 2010, by and among the Company, Codexis Mayflower Holdings, LLC and Maxygen, Inc.

(incorporated by reference to Exhibit 2.1 to the Company’s Current Report on Form 8-K, filed on October 28, 2010).

Employment Agreement by and between the Company and Ross Taylor effective as of August 4, 2019 (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 on November 6, 2019).

Transition and Separation Agreement by and between the Company and Ross Taylor, dated as of February 3, 2023 (incorporated by reference to Exhibit 10.8B to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Employment Agreement by and between the Company and John Nicols effective as of May 28, 2012 (incorporated by reference to Exhibit 10.2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2012, filed on August 9, 2012).

Amendment to Employment Agreement between the Company and John Nicols, dated April 21, 2016 (incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2016, filed on August 9, 2016).

Amendment to Employment Agreement between the Company and John Nicols, dated November 16, 2017 (incorporated by reference to Exhibit 10.8E to the Company’s Annual Report on Form 10-K for the year ended December 31, 2017, filed on March 15, 2018).

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).

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).

Acquisition Agreement by and among the Company, Societé des Produits Nestlé S.A., formerly known as Nestec Ltd.

10.7A Acquisition Agreement by and among the Company, Societé des Produits Nestlé S.A., formerly known as Nestec Ltd.

(“Nestlé Health Science”), effective as of December 26, 2023.

(incorporated by reference to Exhibit 10.

11 to the Company’s Annual Report on Form 10-K for the year ended December 31, 20 23 , filed on February 28, 2024 ).

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).

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).

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.

2 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2023, filed on November 3, 2023).

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).

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).

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).

Offer Letter by and between the Company and Sriram Ryali dated as of December 30, 2023 (incorporated by reference to Exhibit 10.

2 3A to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

Change in Control Severance Agreement by and between the Company and Sriram Ryali dated January 27, 2023 (incorporated by reference to Exhibit 10.

23B to the Company's Annual Report on Form 10-K for the year ended December 31, 2022, filed on February 27, 2023).

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

Loan and Security Agreement by and between the Company and Innovatus Life Sciences Fund I, LP., effective as of February 13, 2024 (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).

First Amendment to the Loan and Security Agreement , dated May 1, 2024, by and between the Company and Innovatus Life Sciences Fund I, LP .

(incorporated by reference to Exhibit 10.

1 to the Company's Quarterly Report on Form 10-Q for the quarter ended June 30, 2024 , filed on A u gust 8, 2024 ).

Second Amendment to the Loan and Security Agreement, dated December 20 , 2024, by and between the Company and Innovatus Life Sciences Fund I, LP.

(incorporated by reference to Exhibit 10.11 to the Company’s Annual Report on Form 10-K for the year ended December 31, 2023, filed on February 28, 2024).

10.7B Amendment No .

1 to the Acquisition Agreement by and between the Company and Nestlé Health Science, effective as of February 28, 2025 (incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2025, filed on May 14, 2025).

10.8A+ 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).

10.8B+ Transition Agreement by and between the Company and Stephen Dilly dated November 5, 2025.

10.9A+ 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).

10.9B+ 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).

10.9C+ Separation and Consulting Agreement by and between the Company and Kevin Norrett dated November 6, 2025.

10.10A Loan and Security Agreement by and between the Company and Innovatus Life Sciences Fund I, LP., effective as of February 13, 2024 (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).

10.10B First Amendment to the Loan and Security Agreement, dated May 1, 2024, by and between the Company and Innovatus Life Sciences Fund I, LP.

(incorporated by reference to Exhibit 10.1 to the Company's Quarterly Report on Form 10-Q for the quarter ended June 30, 2024, filed on August 8, 2024).

10.10C Second Amendment to the Loan and Security Agreement, dated December 20, 2024, by and between the Company and Innovatus Life Sciences Fund I, LP.

(incorporated by reference to Exhibit 10.16C to the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 filed on February 27, 2025).

10.10D Third Amendment to the Loan and Security Agreement dated September 30, 2025, by and between the Company and Innovatus Life Sciences Fund I, LP.

(incorporated by reference to Exhibit 10.1 to the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2025, filed on November 6, 2025) .

10.11+ Codexis, Inc.

1 unchanged sentence

333-281429) filed with the SEC on August 9, 2024).

Offer Letter by and between the Company and Georgia Erbez, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.

3 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024 , filed on October 31 , 2024).

Change in Control Severance Agreement by and between the Company and Georgia Erbez, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.

4 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, filed on October 31, 2024).

Offer Letter by and between the Company and Alison Moore, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.

5 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, filed on October 31, 2024).

Change in Control Severance Agreement by and between the Company and Alison Moore, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.

6 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, filed on October 31, 2024).

19.1 C odexis Insider Trading P olicy effective as of May 9, 2024

10.12A+ Offer Letter by and between the Company and Georgia Erbez, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.3 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, filed on October 31, 2024).

10.13A+ Offer Letter by and between the Company and Alison Moore, dated as of September 30, 2024.

(incorporated by reference to Exhibit 10.5 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2024, filed on October 31, 2024).

10.13B+ Offer Letter by and between the Company and Alison Moore, dated as of November 5, 2025.

10.14+ Offer Letter by and between the Company and Stefan Lutz , dated as of November 5, 2025.

19.1 Codexis Insider Trading Policy effective as of May 9, 2024 incorporated by reference to Exhibit 19.1 to the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 filed on February 27, 2025).

23.1 Consent of KPMG LLP, independent registered public accounting firm.

Consent of BDO USA, P.C.

, independent registered public accounting firm.

Consent of BDO USA, P.C., independent registered public accounting firm.

24.1 Power of Attorney (see signature page to this Annual Report on Form 10-K).

5 unchanged sentences

101 The following materials from Registrant’s Annual Report on Form 10-K for the fiscal year ended December 31, 2025 formatted in Inline Extensible Business Reporting Language (iXBRL) includes:

(i) Consolidated Balance Sheets at December 31, 2024 and December 31, 2023, (ii) Consolidated Statements of Operations for the years ended December 31, 2024, December 31, 2023 and December 31, 2022, (iii) Consolidated Statements of Cash Flows for the years ended December 31, 2024, December 31, 2023 and December 31, 2022, (vi) Consolidated Statements of Stockholders’ Equity for the years ended December 31, 2023, December 31, 2023 and December 31, 2022 and (vii) Notes to Consolidated Financial Statements.

(i) Consolidated Balance Sheets at December 31, 2025 and December 31, 2024, (ii) Consolidated Statements of Operations for the years ended December 31, 2025, December 31, 2024 and December 31, 2023, (iii) Consolidated Statements of Cash Flows for the years ended December 31, 2025, December 31, 2024 and December 31, 2023, (iv) Consolidated Statements of Stockholders’ Equity for the years ended December 31, 2025, December 31, 2024 and December 31, 2023, and (v) Notes to Consolidated Financial Statements.

101.SCH Inline XBRL Taxonomy Extension Schema Document

8 unchanged sentences

** Pursuant to Item 601(b)(32) of Regulation S-K this exhibit is furnished rather than filed with this report.

*** Portions of the exhibit, marked by brackets, have been omitted because the omitted information is (i) not material and (ii) customarily and actually treated as private or confidential.

*** Portions of the of the exhibit, marked by brackets, have been omitted because the omitted information is (i) not material and (ii) customarily and actually treated as private or confidential.

FORM 10-K SUMMARY

2 unchanged sentences

CODEXIS, INC.

February 27, 2025 By:

/s/ Stephen Dilly

Chairman of the Board of Directors, President, and Chief Executive Officer

March 11, 2026 By:

/s/ Alison Moore

President and Chief Executive Officer

(Principal Executive Officer)

POWER OF ATTORNEY

Each person whose individual signature appears below hereby authorizes and appoints Stephen Dilly and Georgia Erbez, and each of them, with full power of substitution and resubstitution and full power to act without the other, as his or her true and lawful attorney-in-fact and agent to act in his or her name, place and stead and to execute in the name and on behalf of each person, individually and in each capacity stated below, and to file any and all amendments to this annual report on Form 10-K and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing, ratifying and confirming all that said attorneys-in-fact and agents or any of them or their or his substitute or substitutes may lawfully do or cause to be done by virtue thereof.

Each person whose individual signature appears below hereby authorizes and appoints Alison Moore and Georgia Erbez, and each of them, with full power of substitution and resubstitution and full power to act without the other, as his or her true and lawful attorney-in-fact and agent to act in his or her name, place and stead and to execute in the name and on behalf of each person, individually and in each capacity stated below, and to file any and all amendments to this annual report on Form 10-K and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing, ratifying and confirming all that said attorneys-in-fact and agents or any of them or their or his substitute or substitutes may lawfully do or cause to be done by virtue thereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated.

SIGNATURE TITLE DATE

/s/ Stephen Dilly Chairman of the Board of Directors, President, and Chief Executive Officer (Principal Executive Officer)

February 27, 2025

Stephen Dilly

/s/ Georgia Erbez Chief Financial Officer (Principal Financial and Accounting Officer) Date:

February 27, 2025

/s/ Alison Moore President and Chief Executive Officer (Principal Executive Officer) and Director Date:

March 11, 2026

/s/ Georgia Erbez Chief Financial Officer and Chief Business Officer (Principal Financial and Accounting Officer) Date:

March 11, 2026

Georgia Erbez

/s/ Stephen Dilly Executive Chair Date:

March 11, 2026

Stephen Dilly

/s/ Raymond De Vré Director Date:

February 27, 2025

March 11, 2026

Raymond De Vré

Dorgan Director Date:

February 27, 2025

/s/ Cynthia Collins Director Date:

March 11, 2026

Cynthia Collins

/s/ Esther Martinborough Director Date:

February 27, 2025

March 11, 2026

Esther Martinborough

Stewart Parker Director Date:

February 27, 2025

March 11, 2026

Stewart Parker

/s/ Christos Richards Director Date:

February 27, 2025

March 11, 2026

Christos Richards

/s/ Rahul Singhvi Director Date:

February 27, 2025

March 11, 2026

Rahul Singhvi

Smith Director Date:

February 27, 2025

March 11, 2026

/s/ Dennis P.

Wolf Director Date:

February 27, 2025

March 11, 2026

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-K

Item 9A. Controls and Procedures