Exhibit

Exhibit 10.1

Codexis, Inc.

200 Penobscot Drive

Redwood City, CA 94063

Tel: +1 650.421.8100

Fax: +1 650.421.8102

www.codexis.com

You and Codexis, Inc. (the “Company”) are currently parties to a Change of Control Severance Agreement, dated as of February 28, 2014 (the “CoC Agreement”), which provides that you will be entitled to receive certain severance payments and benefits upon certain qualifying terminations of employment. Effective as of the date of this amendment (this “Amendment”), you and the Company hereby agree to amend the CoC Agreement as follows:

“Notwithstanding the foregoing, any outstanding performance stock units held by Executive shall automatically become vested with respect to: (i) in the event of a Change of Control that occurs prior to the applicable Measurement Date, such number of shares of Company common stock corresponding to the target performance level for any applicable performance goals; or (ii) in the event of a Change of Control that occurs on or after the Measurement Date, such number of shares of Company common stock corresponding to the Company’s actual achievement of any applicable performance goals.”

“For purposes of determining the number of shares subject to any outstanding performance stock units that would otherwise vest on the next vesting date pursuant to the foregoing sentence, the applicable performance goals shall be deemed achieved: (i) in the event of a Change of Control that occurs prior to the applicable Measurement Date, at the target performance level; or (ii) in the event of a Change of Control that occurs on or after the Measurement Date, based on the Company’s actual achievement.”

“Measurement Date. ‘Measurement Date’, with respect to an award of performance stock units, shall mean the date the Compensation Committee of the Board of Directors determines the final performance factor for the applicable performance period.”

All terms and provisions of the CoC Agreement not amended hereby, either expressly or by necessary implication, shall remain in full force and effect. From and after the date of this Amendment, all references

to the term “CoC Agreement” in this Amendment or the original CoC Agreement shall include the terms contained in this Amendment.

Please indicate your acceptance of and agreement to the terms and conditions set forth in this Amendment by signing in the space below and returning the executed Amendment to the Company.