Document:

Change in Control Agreement - Robert S. Breuil

 Exhibit 10.13B 
 CODEXIS, INC. 
 CHANGE
OF CONTROL AGREEMENT 
 This CHANGE OF
CONTROL AGREEMENT (the “Agreement”), dated January 3, 2003, is made by and between CODEXIS, INC., a Delaware corporation (the “Company”),
and Robert (Bubba) Breuil (the “Executive”). 
 WHEREAS, the Company considers it
essential to the best interests of its stockholders to foster the continuous employment of key management personnel; 
 WHEREAS, the Board of Directors of the Company recognizes that, as is the case with many corporations, the possibility of a Change of Control (as defined herein) exists and that such possibility, and the
uncertainty and questions that it may raise among management, may result in the departure or distraction of management personnel to the detriment of the Company and its stockholders; and 
 WHEREAS, the Board has determined that appropriate steps should be taken to reinforce and encourage the
continued attention and dedication of members of the Company’s management, including the Executive, to their assigned duties without distraction in the face of potentially disturbing circumstances arising from the possibility of a Change of
Control. 
 NOW, THEREFORE, in consideration of the premises and the mutual
covenants herein contained, the Company and the Executive agree as follows: 
 1. Introduction; Purposes. 
 (a) The purpose of this Agreement is to provide the Executive with protection of certain benefits in case of a termination of his or her
employment with the Company in connection with a Change of Control of the Company. 
 (b) The Company, by means of the
Agreement, seeks to (i) secure and/or retain the services of the Executive and (ii) provide incentives for the Executive to exert maximum efforts for the success of the Company even in the face of a potential Change of Control of the
Company. 

 2. Definitions. 
 (a) “Accountants” has the meaning given thereto in Section 4. 
 (b)
“ADEA” has the meaning given thereto in Section 5(c). 
 (c) “Agreement” means this Change of Control
Agreement. 
 (d) “Board” means the Board of Directors of the Company. 
 (e) “Cause” means the Executive’s: (i) willful and continued failure to substantially perform the Executive’s
duties with the Company (other than as a result of physical or mental disability) after a written demand for substantial performance is deliver to the Executive by the Company, which demand specifically identifies the manner in which the Company
believes that the Executive has not substantially performed the Executive’s duties and that has not been cured within fifteen (15) days following receipt by the Executive of the written demand; (ii) commission of a felony (other than
a traffic-related offense) that in the written determination of the Company is likely to cause or has caused material injury to the Company’s business; (iii) dishonesty with respect to a significant matter relating to the Company’s
business; or (iv) material breach of any agreement by and between the Executive and the Company, which material breach has not been cured within fifteen (15) days following receipt by the Executive of written notice from the Company
identifying such material breach. 
 (f) “Change of Control” means: (i) a dissolution or liquidation of the
Company; (ii) a sale of all or substantially all the assets of the Company; (iii) a merger or consolidation in which the Company is not the surviving corporation and in which beneficial ownership of securities of the Company representing
at least fifty percent (50%) of the combined voting power entitled to vote in the election of directors has changed; (iv) a reverse merger in which the Company is the surviving corporation but the shares of the common stock of the Company
outstanding immediately before the merger are converted by virtue of the merger into other property, whether in the form of securities, cash or otherwise, and in which beneficial ownership of securities of the Company representing at least fifty
percent (50%) of the combined voting power entitled to vote in the election of directors has changed; (v) an acquisition by any person, entity or group within the meaning of Section 13(d) or 14(d) of the Exchange Act, or any
comparable successor provisions (excluding any employee benefit plan, or related trust, sponsored or maintained by the Company or subsidiary of the Company or other entity controlled by the Company) of the beneficial ownership (within the meaning of
Rule 13d-3 promulgated under the Exchange Act, or comparable successor rule) of securities of the Company representing at least fifty percent (50%) of the combined voting power entitled to vote in the election of directors; or, (vi) in the
event that the individuals who are members of the Incumbent Board cease for any reason to constitute at least fifty percent (50%) of the Board. Notwithstanding the foregoing, a Change of Control shall not include any transaction effected
primarily for the purpose of financing the Company with cash (as determined by the Committee acting in good faith and without regard to whether such transaction is effectuated by a merger, equity financing or otherwise). 
  

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 (g) “Code” means the Internal Revenue Code of 1986, as amended. 
 (h) “Committee” means the Compensation Committee of the Board or such other committee as appointed by the Board to administer this
Agreement. 
 (i) “Company” means Codexis, Inc., a Delaware corporation. 
 (j) “Company-Paid Coverage” has the meaning given thereto in Section 3(a). 
 (k) “Confidential Information, Secrecy and Invention Agreement” has the meaning given thereto in Section 5(b). 
 (l) “Disability” means the Executive’s physical or mental disability that prevents the Executive from satisfactorily
performing the normal duties and responsibilities of the Executive’s office in the good faith determination of the Committee for a period of more than one hundred twenty (120) consecutive days. 
 (m) “Effective Date” means the date first above written. 
 (n) “Employee Agreement and Release” has the meaning given thereto in Section 5(c). 
 (o) “Exchange Act” means the Securities Exchange Act of 1934, as amended. 
 (p) “Excise Tax” has the meaning given thereto in Section 4. 
 (q) “Executive” means the person identified in the introductory paragraph of this Agreement. 
 (r) “Good Reason” means: (i) any material reduction of the Executive’s duties, authority or responsibilities relative to
the Executive’s duties, authority, or responsibilities as in effect immediately before such reduction, except if agreed to in writing by the Executive; (ii) a reduction by the Company in the base salary of the Executive, or of twenty-five
percent (25%) or more in the Target Bonus opportunity of such Executive, as in effect immediately before such reduction, except if agreed to in writing by the Executive; (iii) the relocation of the Executive to a facility or a location
more than thirty (30) miles from the Executive’s then present business location, except if agreed to in writing by the Executive; (iv) a material breach by the Company of any provision of this Agreement or (v) any failure of the
Company to obtain the assumption of this Agreement by any successor or assign of the Company. 
 (s) “Incumbent Board”
means the individuals who, as of the Effective Date, are members of the Board. If the election, or nomination for election by the Company’s stockholders, of any new director is approved by a vote of at least fifty percent (50%) of the
Incumbent Board, such new director shall be considered as a member of the Incumbent Board. 
  

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 (t) “Section 16 Officer” means an “officer” of the Company, as defined
in Rule 16a-1(f) promulgated under the Exchange Act, designated as such by action of the Board, and shall include an individual who would be a Section 16 Officer but for the fact that the Company is not subject to the reporting requirements of
the Exchange Act. 
 (u) “Target Bonus” means the Executive’s target bonus for the then current fiscal year, as
set by the Board or the appropriate committee thereof. 
 3. Severance Benefits in the Event of a Change of Control. 
 (a) If within eighteen (12) months following the date of a Change of Control of the Company either (i) the Company terminates the
Executive’s employment other than for Cause, death or Disability or (ii) the Executive terminates his or her employment with the Company voluntarily with Good Reason, then in each case, subject to Section 4 and Section 5:
(i) the Executive shall be entitled to receive a lump sum payment equal to one times the Executive’s yearly base salary in effect on the date of termination (without giving effect to any reduction in base salary subsequent to a Change of
Control that constitutes Good Reason), (ii) each of the Executive’s outstanding stock options, all stock subject to repurchase, restricted stock awards and restricted stock purchases, and any options, stock subject to repurchase, awards or
purchases held in the name of an estate planning vehicle for the benefit of the Executive or his or her immediate family, shall have their vesting and exercisability schedule accelerate in full (or, as applicable, the corresponding repurchase right
shall lapse in full) as of the date of termination; (iii) if on the date of termination the Executive is covered by any Company-paid health, disability, accident and/or life insurance plans or programs, the Company shall provide to the
Executive benefits substantially similar to those that the Executive was receiving immediately prior to the date of termination (the “Company-Paid Coverage”). If such coverage included the Executive’s spouse and/or dependents
immediately prior to the date of termination, such spouse and/or dependents shall also be covered at Company expense. Company-Paid Coverage shall continue until the earlier of (x) one (1) year from the date of termination, or (y) the
date that the Executive and his or her spouse and/or dependents become covered under another employer’s health, disability, accident and/or life insurance plans or programs that provides the Executive and his or her spouse and/or dependents
with comparable benefits and levels of coverage. 
 (b) If within twelve (12) months following the date of a Change of
Control of the Company the Executive’s employment with the Company is terminated as a result of death or Disability, then in each case, subject to Section 4 and Section 5: (i) each of the Executive’s outstanding stock
options, all stock subject to repurchase, restricted stock awards and restricted stock purchases, and any options, stock subject to repurchase, awards or purchases held in the name of an estate planning vehicle for the benefit of the Executive or
his or her immediate family, shall have their vesting and exercisability schedule accelerated such that vesting (or, as applicable, the corresponding repurchase right lapsing) shall occur as if the vesting (or lapsing) had occurred on a monthly
basis from the last date of vesting (or lapse) to the date of termination; and (ii) the Company will provide the Executive with health, disability, accident and/or life insurance benefits as described in Section 3(a)(iii). 
  

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 (c) In no event shall the Executive be obligated to seek other employment or take any other
action to mitigate the amounts payable to the Executive under this Agreement. 
 (d) The Executive’s employment shall be
deemed to have been terminated following a Change of Control by the Company without Cause or by the Executive with Good Reason if the Executive’s employment is terminated prior to a Change of Control without Cause at the direction of a person
who has entered into an agreement with the Company the consummation of which will constitute a Change of Control or if the Executive terminates his or her employment with Good Reason prior to a Change of Control if the circumstances or event that
constitutes Good Reason occurs at the direction of such person. 
 4. Parachute Payments; Excise Tax. 
 In the event that the severance, acceleration of stock options and other benefits payable to the Executive under this Agreement or otherwise
as a result of a Change of Control of the Company (i) constitute “parachute payments” within the meaning of Section 280G (as it may be amended or replaced) of the Code and (ii) but for this Section 4, would be subject
to the excise tax imposed by Section 4999 (as it may be amended or replaced) of the Code (the “Excise Tax”), then the Executive’s benefits payable in connection therewith shall be either 
 (a) delivered in full, or 
 (b) delivered as to such lesser extent that would result in no portion of such benefits being subject to the Excise Tax, whichever of the foregoing amounts, taking into account the applicable federal, state and local income taxes and the
Excise Tax, results in the receipt by the Executive on an after-tax basis, of the greatest amount of benefits, notwithstanding that all or some portion of such benefits may be taxable under the Excise Tax. Unless the Company and the Executive
otherwise agree in writing, any determination required under this Section 4 shall be made in writing in good faith by the outside accounting firm responsible for auditing the Company’s financial records (the “Accountants”). In
the event of a reduction in benefits hereunder, the Executive shall be given the choice of which benefits to reduce. For purposes of making the calculations required by this Section 4, the Accountants may make reasonable assumptions and
approximations concerning applicable taxes and may rely on reasonable, good faith interpretations concerning the application of the Code. 
 The Company and the Executive shall furnish to the Accountants such information and documents as the Accountants may reasonably request in order to make a determination under this Section 4. The
Company shall bear all costs the Accountants may reasonably incur in connection with any calculations contemplated by this Section 4. 
  

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 5. Limitations and Conditions on Benefits. 
 The benefits and payments provided under this Agreement shall be subject to the following terms and limitations: 
 (a) Withholding Taxes. The Company shall withhold required federal, state and local income and employment taxes from any payments
hereunder. 
 (b) Confidential Information, Secrecy and Invention Agreement Prior to Receipt of Benefits. The Executive
shall have executed and delivered to the Company a standard form of the Company’s confidential information, secrecy and invention agreement, a copy of the current form of which is attached as Exhibit A (the “Confidential Information,
Secrecy and Invention Agreement”), prior to the receipt or provision of any benefits (including the acceleration benefits) under this Agreement. Additionally, the Executive agrees that all documents, records, apparatus, equipment and other
physical property that is furnished to or obtained by the Executive in the course of his or her employment with the Company shall be and shall remain the sole property of the Company. The Executive agrees not to make or retain copies, reproductions
or summaries of any such property, except as otherwise necessary while acting in the normal course of business. In the event of any material breach by the Executive of the Confidential Information, Secrecy and Invention Agreement that is not cured
within thirty (30) days of notice of such breach to the Executive, all benefits payable under Section 4 of this Agreement shall immediately terminate. 
 (c) Employee Agreement and Release Prior to Receipt of Benefits. If the Executive’s employment with the Company terminates involuntarily other than for Cause, death or Disability, or the
Executive terminates his or her employment with the Company voluntarily with Good Reason, then prior to, and as a condition of the receipt of any benefits (including the acceleration of benefits) under this Agreement on account of such termination,
the Executive shall, as of the date of such termination, execute an employee agreement and release in the form attached as Exhibit B (the “Employee Agreement and Release”) prior to receipt of benefits. Such Employee Agreement and Release
shall specifically relate to all the Executive’s rights and claims in existence at the time of such execution and shall confirm the Executive’s obligations under the Company’s standard form of Confidential Information, Secrecy and
Invention Agreement. If and only if the Executive is covered by the federal Age Discrimination in Employment Act of 1967, as amended (“ADEA”) (currently all those 40 years of age or over on the date of termination), the Executive has
twenty-one (21) days to consider whether to execute such Employee Agreement and Release and the Executive may revoke such Employee Agreement and Release within seven (7) days after execution of such Employee Agreement and Release. In the
event the Executive is covered by ADEA and does not execute such Employee Agreement and Release within the twenty-one (21) days specified above, or if the Executive revokes such Employee Agreement and Release within the seven (7) day
period specified above, no benefits (including the acceleration benefits) under Section 3 of this Agreement shall be payable or made available to the Executive on account of a termination. 
  

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 6. Termination. Prior to a Change of Control of the Company, this Agreement shall
automatically terminate on the date the Executive ceases to be a Section 16 Officer, as evidenced by action of the Board removing the Executive as a Section 16 Officer or otherwise; provided, however, that if the Executive ceases to be a
Section 16 Officer prior to a Change of Control at the direction of a person who has entered into an agreement with the Company the consummation of which will constitute a Change of Control, this Agreement shall not terminate due to the change
in status of the Executive. 
 7. At-Will Employment. The Company and the Executive acknowledge that the Executive’s
employment is and shall continue to be at-will, as defined under applicable law. This Agreement shall not be construed as creating an express or implied contract of employment between the Executive and the Company. The Executive shall not have any
right to be retained in the employment of the Company. 
 8. Notices. Any notice provided under this Agreement shall be
in writing and shall be deemed to have been effectively given (i) upon receipt when delivered personally, (ii) one day after sending when sent by express mail service (such as Federal Express), or (iii) five (5) days after
sending when sent by regular mail to the following address: 
 In the case of the Company: 
 Codexis, Inc. 
 200 Penobscot Drive 
 Redwood City, CA 94063 
 Attn: Human Resources 
 In the case of the Executive: 
 Robert (Bubba) Breuil 
 [Address] 
 or to such other
address as the Company or the Executive hereafter designates by written notice in accordance with this Section 8. 
 9.
Litigation/Arbitration Expenses. Reasonable litigation and/or arbitration costs and expenses shall be paid by the Company, win or lose, in connection with any dispute between the Company (and its successors) and the Executive concerning this
Agreement; provided, however, that if the litigation or arbitration is found to have been commenced in bad faith by the Executive, the Executive shall bear all of his or her own costs and expenses in connection with such litigation or arbitration.

 10. Successors and Assigns. This Agreement is intended to bind and inure to the benefit of and be enforceable by the
Executive, and the Company, and any surviving entity resulting from a Change of Control and upon any other person who is a successor by merger, acquisition, consolidation or otherwise to the business formerly carried on by the Company, and their
respective successors, assigns, heirs, executors and administrators, without regard to whether or not such person actively assumes any rights or duties hereunder; provided, however, that the Executive may not assign any duties hereunder without the
prior written consent of the Company. 
  

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 11. Miscellaneous. 
 (a) No provision of this Agreement may be modified, waived or discharged unless such waiver, modification or discharge is agreed to in
writing by each of the parties. 
 (b) No agreements or representations, oral or otherwise, express or implied, with respect to
the subject matter hereof have been made by either party that are not expressly set forth in this Agreement. 
 (c) The
invalidity or unenforceability of any provision of this Agreement shall not affect the validity or enforceability of any other provision of this Agreement, which shall remain in full force and effect. 
 12. Governing Law. This Agreement shall be governed by, and construed in accordance with, the laws of the State of California,
regardless of the law that might be applied under applicable principles of conflicts of law. 
 13. Entire Understanding.
This Agreement constitutes the entire agreement and understanding between the parties hereto with respect to the termination of the Executive’s employment after a Change of Control, and supersedes all other prior agreements, representations and
understandings, both written and oral, between the parties hereto with respect to the subject matter hereof. The Executive agrees that the Change of Control Agreement between the Executive and Maxygen, Inc. is terminated and null and void as of the
date of this Agreement. 
  

			
	CODEXIS, INC.
		
	By:	 	 /s/ Alan Shaw

	Name:	 	Alan Shaw
	Title:	 	President and CEO
	
	THE EXECUTIVE
	
	 /s/ Robert (Bubba) Breuil

	Name:	 	Robert (Bubba) Breuil

  

 8Separation Agreement - Robert S. Breuil

 Exhibit 10.13C 
 Confidential 
 SEPARATION AGREEMENT

 This Separation Agreement (the “Agreement”) by and between Robert S. Breuil
(“Executive”) and Codexis, Inc., a Delaware corporation (the “Company”), is made effective as of the eighth (8th) day following the date Executive signs this Agreement with reference to the following facts: 
 A. Executive’s employment with the Company and status as an officer and employee of the Company and each of its affiliates will end
effective upon the Termination Date (as defined below). 
 B. Executive and the Company want to end their relationship amicably
and also to establish the obligations of the parties including, without limitation, all amounts due and owing to Executive. 
 NOW, THEREFORE, in consideration of the mutual covenants and agreements hereinafter set forth, the parties agree as follows: 
 1. Termination Date. Executive acknowledges and agrees that his status as an officer and employee of the Company and as an officer and/or director of the Company’s subsidiaries will end
effective as of June 30, 2009 (the “Termination Date”). Executive hereby agrees to execute such further document(s) as shall be determined by the Company as necessary or desirable to give effect to the termination of
Executive’s status as an officer and, if applicable, director of the Company and each of its subsidiaries; provided that such documents shall not be inconsistent with any of the terms of this Agreement. 
 2. Final Paycheck. On the Termination Date, the Company will pay Executive all accrued but unpaid base salary and the
value of all accrued and unused vacation earned through the Termination Date, subject to standard payroll deductions and withholdings. In addition, the Company shall reimburse Executive for all outstanding expenses incurred prior to the Termination
Date which are consistent with the Company’s policies in effect from time to time with respect to travel, entertainment and other business expenses, subject to the Company’s requirements with respect to reporting and documenting such
expenses. Executive is entitled to the payments set forth in this Section 2 regardless of whether Executive executes this Agreement. 
 3. Separation Payments and Benefits. Without admission of any liability, fact or claim, the Company hereby agrees, subject to Executive signing and delivering to the Company this Agreement by 5:00
p.m. (PDT) on August 6, 2009, this Agreement becoming no longer subject to revocation as provided in Section 5(c)(iii) and Executive’s performance of his continuing obligations pursuant to this Agreement and that certain Confidential
Information, Secrecy, and Invention Agreement entered into between Executive and the Company as of January 3, 2006 (the “Confidentiality Agreement”), to provide Executive the severance benefits set forth below. Specifically,
the Company and Executive agree as follows: 
 (a) Severance Pay. As soon as administratively practicable
after this Agreement becomes no longer subject to revocation and no later than thirty (30) days thereafter, the Company shall pay to Executive a lump sum cash amount equal to $160,000, which represents six (6) months of Executive’s
base salary, subject to any applicable withholding obligations. 
 (b) Healthcare Continuation Coverage.
If Executive elects to receive continued healthcare coverage pursuant to COBRA, the Company shall reimburse Executive

  

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 Confidential 
  

 
for the premiums paid by Executive for Executive and Executive’s covered dependents during the period commencing on the Termination Date and ending on the six month anniversary of the
Termination Date or such earlier date that Executive and/or Executive’s covered dependents become no longer eligible for COBRA, provided that Executive submits documentation to the Company substantiating his payments for COBRA coverage. Any
such reimbursement payments shall be made to Executive no later than ten days after Executive’s submission of documentation to the Company substantiating his payments for COBRA coverage. After the Company ceases to reimburse premiums pursuant
to the preceding sentence, Executive may, if eligible, elect to continue healthcare coverage at Executive’s expense in accordance with the provisions of COBRA. 
 (c) Stock Options. As of the Termination Date, Executive’s options to purchase shares of the Company’s
common stock shall have vested with respect to 441,527 shares, as set forth on Exhibit A (collectively, the “Vested Stock Options”) pursuant to the terms of the Company’s 2002 Equity Incentive Plan, as amended (the
“Plan”), and the option agreements entered into to evidence such stock options (each such agreement an “Original Option Agreement”). Each Original Option Agreement evidencing Executive’s Vested Stock Options shall be
hereby amended collectively as follows: 
 (i) The Vested Stock Options shall remain exercisable until the
earliest of (a) the third anniversary of the Termination Date, (b) the closing of a Change in Control (as defined in the Plan) of the Company or (c) the later of (A) the six month anniversary of expiration of any
“lock-up” or similar transfer restriction imposed on the shares of any common stock underlying the Vested Stock Options in connection with the initial public offering (the “IPO”) of any class of equity securities of the Company
and (B) the twelve month anniversary of the IPO. This extended exercisability shall not result in the imposition of any taxes on Executive under Section 409A of the Internal Revenue Code of 1986, as amended (the “Code”).

 (ii) In the event of a Change in Control (as defined in the Plan) Executive shall be given notice by the
Company of such Change in Control not later than the earlier of (i) three days following the execution of a definitive agreement which if consummated would constitute such Change in Control or (ii) thirty days prior to the consummation of
such Change in Control; provided that Executive agrees to sign an agreement with the Company to keep such Change in Control transaction confidential prior to the consummation of such Change in Control. 
 (iii) Executive acknowledges that upon the execution of this Agreement, each unexercised “incentive stock option”
within the meaning of Section 422 of the Code shall be deemed modified for the purposes of Section 424 of the Code and, to the extent the exercise price thereof is lower than the fair market value of the Company’s common stock as of
the date this Agreement is executed, such option shall no longer qualify as an incentive stock option and Executive will lose the potentially favorable tax treatment associated with such option. 
 (iv) If Executive desires to exercise any Vested Stock Options, Executive must follow the procedures set forth in
Executive’s Original Option Agreements, including payment of the exercise price and any withholding obligations. If by the earliest date specified above in this Section 3(c)(i) the Company has not received a duly executed notice of
exercise and remuneration in accordance with Executive’s Original Option Agreements, Executive’s Vested Stock Options shall automatically terminate and be of no further effect. 
  

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 Confidential 
  

 (v) Effective on the Termination Date, all of Executive’s options
to purchase an aggregate of 298,973 shares of Company common stock that were not then fully vested (as derived from the differences between the “Total Option Shares” and “Vested as of June 30, 2009” figures on Exhibit A) are
hereby terminated 
 (d) Taxes. Executive understands and agrees that all payments under this
Section 3 will be subject to appropriate tax withholding and other deductions. To the extent any taxes may be payable by Executive for the benefits provided to him by this Agreement beyond those withheld by the Company, Executive agrees to pay
them himself and to indemnify and hold the Company and the other entities released herein harmless for any tax claims or penalties, and associated attorneys’ fees and costs, resulting from any failure by him to make required payments. To the
extent that any reimbursements payable pursuant to this Agreement are subject to the provisions of Section 409A of the Code, such reimbursements shall be paid to Executive no later than December 31 of the year following the year in which
the expense was incurred, the amount of expenses reimbursed in one year shall not affect the amount eligible for reimbursement in any subsequent year, and Executive’s right to reimbursement under this Agreement will not be subject to
liquidation or exchange for another benefit. 
 (e) Sole Separation Benefit. Executive agrees that the
payments provided by this Section 3 are not required under the Company’s normal policies and procedures and are provided as a severance payment solely in connection with this Agreement. Executive acknowledges and agrees that the payments
referenced in this Section 3 constitute adequate and valuable consideration, in and of themselves, for the promises contained in this Agreement. 
 (f) Continued Obligations. Executive acknowledges and agrees that Executive shall continue to be subject to, and abide by, the Confidentiality Agreement. 
 4. Full Payment. Executive acknowledges that the payment and arrangements herein shall constitute full and complete
satisfaction of any and all amounts properly due and owing to Executive as a result of his employment with the Company and the termination thereof. Executive further acknowledges that, other than the Confidentiality Agreement, this Agreement shall
supersede each agreement entered into between Executive and the Company regarding Executive’s employment, including, without limitation, Executive’s offer letter agreement with the Company (the “Offer Letter”) and
Executive’s Amended and Restated Change of Control Severance Agreement (the “Change of Control Agreement”), and each such agreement other than the Original Option Agreements shall be deemed terminated and of no further effect
as of the Termination Date. 
 5. Executive’s Release of the Company. Executive understands that by
agreeing to the release provided by this Section 5, Executive is agreeing not to sue, or otherwise file any claim against, the Company or any of its employees, directors or other agents for any reason whatsoever based on anything that has
occurred as of the date Executive signs this Agreement. The Company acknowledges that as of the date hereof it is not aware of any claims, either unasserted or asserted, that it may have against Executive in equity, or under local, state or federal
law or regulation, or the laws and regulations of the foreign jurisdictions. 
  

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 Confidential 
  

 (a) Full Release. On behalf of Executive and Executive’s
heirs and assigns, Executive hereby releases and forever discharges the “Releasees” hereunder, consisting of the Company, and each of its owners, affiliates, subsidiaries, predecessors, successors, assigns, agents, directors,
officers, partners, employees, and insurers, and all persons acting by, through, under or in concert with them, or any of them, of and from any and all manner of action or actions, cause or causes of action, in law or in equity, suits, debts, liens,
contracts, agreements, promises, liability, claims, demands, damages, loss, cost or expense, of any nature whatsoever, known or unknown, fixed or contingent (hereinafter called “Claims”), which Executive now has or may hereafter
have against the Releasees, or any of them, by reason of any matter, cause, or thing whatsoever from the beginning of time to the date hereof, including, without limiting the generality of the foregoing, any Claims arising out of, based upon, or
relating to Executive’s hire, employment, remuneration or resignation by the Releasees, or any of them, including any Claims arising under Title VII of the Civil Rights Act of 1964, as amended, 42 U.S.C. § 2000, et seq.; Americans
with Disabilities Act, as amended, 42 U.S.C. § 12101 et seq.; the Rehabilitation Act of 1973, as amended, 29 U.S.C. § 701 et seq.; Age Discrimination in Employment Act, as amended, 29 U.S.C. § 621, et seq.;
Civil Rights Act of 1866, and Civil Rights Act of 1991; 42 U.S.C. § 1981, et seq.; Equal Pay Act, as amended, 29 U.S.C. § 206(d); regulations of the Office of Federal Contract Compliance, 41 C.F.R. Section 60, et seq.; The
Family and Medical Leave Act, as amended, 29 U.S.C. § 2601 et seq.; the Fair Labor Standards Act of 1938, as amended, 29 U.S.C. § 201 et seq.; the Employee Retirement Income Security Act, as amended, 29 U.S.C.
§ 1001 et seq.; the Worker Adjustment and Retraining Notification Act, as amended, 29 U.S.C. § 2101 et seq.; the California Fair Employment and Housing Act, as amended, Cal. Lab. Code § 12940 et seq.; the California Equal Pay
Law, as amended, Cal. Lab. Code §§ 1197.5(a),199.5; the Moore-Brown-Roberti Family Rights Act of 1991, as amended, Cal. Gov’t Code §§12945.2, 19702.3; California Labor Code §§ 1101, 1102; the California WARN Act,
California Labor Code §§ 1400 et. seq; California Labor Code §§ 1102.5(a),(b); claims for wages under the California Labor Code and any other federal, state or local laws of similar effect. 
 (b) Exceptions. Notwithstanding the generality of the foregoing, Executive does not release the following claims:

 (i) Claims for unemployment compensation or any state disability insurance benefits pursuant to the terms of
applicable state law; 
 (ii) Claims for workers’ compensation insurance benefits under the terms of any
worker’s compensation insurance policy or fund of the Company; 
 (iii) Claims to continued participation
in certain of the Company’s group benefit plans pursuant to the terms and conditions of COBRA; 
 (iv)
Claims to any benefit entitlements vested as the date of Executive’s employment termination, pursuant to written terms of any Company employee benefit plan; 
 (v) Claims for indemnification under California Labor Code Section 2802, the Company’s Certificate of
Incorporation, the Company’s Bylaws or the Delaware General Corporation Law; 
  

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 Confidential 
  

 (vi) Executive’s right to bring to the attention of the Equal
Employment Opportunity Commission claims of discrimination; provided, however, that Executive does release Executive’s right to secure any damages for alleged discriminatory treatment; and 
 (vii) Any other Claim that may not be released by private agreement. 
 (c) Acknowledgement. In accordance with the Older Workers Benefit Protection Act of 1990, Executive has been advised
of the following: 
 (i) Executive should consult with an attorney before signing this Agreement; 
 (ii) Executive has been given at least twenty-one (21) days to consider this Agreement; 
 (iii) Executive has seven (7) days after signing this Agreement to revoke it. If Executive wishes to revoke this
Agreement, Executive must deliver notice of Executive’s revocation in writing, no later than 5:00 p.m. on the 7th day following Executive’s execution of this Agreement to Andy Danforth, V.P. Human Resources, 200 Penobscot Drive, Redwood
City, California 94063, fax: (650) 421-8145. Executive understands that if he revokes this Agreement, it will be null and void in its entirety, and he will not be entitled to any payments or benefits provided in this Agreement, other than as
provided in Section 2. 
 (d) California Civil Code Section 1542. EXECUTIVE ACKNOWLEDGES THAT
EXECUTIVE HAS BEEN ADVISED OF AND IS FAMILIAR WITH THE PROVISIONS OF CALIFORNIA CIVIL CODE SECTION 1542, WHICH PROVIDES AS FOLLOWS: 
 “A GENERAL RELEASE DOES NOT EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR SUSPECT TO EXIST IN HIS OR HER FAVOR AT THE TIME OF EXECUTING THE RELEASE, WHICH, IF KNOWN BY HIM OR HER, MUST HAVE MATERIALLY AFFECTED HIS OR HER
SETTLEMENT WITH THE DEBTOR.” 
 BEING AWARE OF SAID CODE SECTION, EXECUTIVE HEREBY EXPRESSLY WAIVES ANY RIGHTS EXECUTIVE
MAY HAVE THEREUNDER, AS WELL AS UNDER ANY OTHER STATUTES OR COMMON LAW PRINCIPLES OF SIMILAR EFFECT. 
 6.
Consulting, Non-Disparagement, Transition, Transfer of Company Property and Limitations on Service. 
 (a) Consulting. During the period of time commencing on the Termination Date and ending on the three month anniversary of the Termination Date, Executive shall be available, on a non-exclusive basis, as a consultant to respond to,
and shall respond with reasonable promptness and completeness to, e-mail and telephone inquiries from the Company regarding transitional matters provided that such inquiries would not interfere in any significant manner with other business pursuits
(including other

  

 5 

 Confidential 
  

 
employment) by Executive. For each hour, or partial hour, of service performed by Executive at the request of the Company pursuant to the preceding sentence, Executive shall be entitled to be
compensated as an independent contractor at the rate of $300. As an independent contractor, Executive understands and agrees that he shall be responsible for any taxes with respect to the amounts paid to him pursuant to this Section 6(a) and
that while performing any services under this Section 6(a) Executive shall not be eligible to participate in or accrue benefits under any Company benefit plan for which status as an employee of the Company is a condition of such participation
or accrual. To the extent that Executive were deemed eligible to participate in any Company benefit plan, he hereby waives his participation. In addition, nothing in this Section 6(a) shall entitle Executive to the vesting of any stock options
or otherwise prevent Executive’s unvested stock options from terminating effective as of the Termination Date. 
 (b) Non-Disparagement. Executive agrees that he shall not disparage, criticize or defame the Company, its affiliates and their respective affiliates, directors, officers, agents, partners, stockholders or employees, either publicly
or privately. The Company agrees that it shall not, and it shall instruct its officers and members of its Board of Directors to not, disparage, criticize or defame Executive, either publicly or privately. Nothing in this Section 6(b) shall have
application to any evidence or testimony required by any court, arbitrator or government agency. 
 (c)
Transition. Each of the Company and Executive shall use their respective reasonable efforts to cooperate with each other in good faith to facilitate a smooth transition of Executive’s duties to other executive(s) of the Company.

 (d) Transfer of Company Property. On or before the Termination Date, Executive shall turn over to the
Company all files, memoranda, records, and other documents, and any other physical or personal property which are the property of the Company and which he had in his possession, custody or control at the time he signed this Agreement. 
 7. Executive Representations. Executive warrants and represents that (a) he has not filed or authorized the
filing of any complaints, charges or lawsuits against the Company or any affiliate of the Company with any governmental agency or court, and that if, unbeknownst to Executive, such a complaint, charge or lawsuit has been filed on his behalf, he will
immediately cause it to be withdrawn and dismissed, (b) he has reported all hours worked as of the date of this Agreement and has been paid all compensation, wages, bonuses, commissions, and/or benefits to which he may be entitled and no other
compensation, wages, bonuses, commissions and/or benefits are due to him, except as provided in this Agreement, (c) he has no known workplace injuries or occupational diseases and has been provided and/or has not been denied any leave requested
under the Family and Medical Leave Act or any similar state law, (d) the execution, delivery and performance of this Agreement by Executive does not and will not conflict with, breach, violate or cause a default under any agreement, contract or
instrument to which Executive is a party or any judgment, order or decree to which Executive is subject, and (e) upon the execution and delivery of this Agreement by the Company and Executive, this Agreement will be a valid and binding
obligation of Executive, enforceable in accordance with its terms. 
 8. No Assignment. Executive warrants
and represents that no portion of any of the matters released herein, and no portion of any recovery or settlement to which Executive might be entitled, has been assigned or transferred to any other person, firm or corporation not a party to this
Agreement, in any manner, including by way of subrogation or operation of law or

  

 6 

 Confidential 
  

 
otherwise. If any claim, action, demand or suit should be made or instituted against the Company or any other Releasee because of any actual assignment, subrogation or transfer by Executive,
Executive agrees to indemnify and hold harmless the Company and all other Releasees against such claim, action, suit or demand, including necessary expenses of investigation, attorneys’ fees and costs. 
 9. Confidentiality. Executive agrees to keep the fact, terms and amount of this Agreement completely confidential, and
not to disclose such information to anyone other than his current and former spouse, attorneys and licensed tax and/or professional investment advisors (hereafter referred to as “Executive’s Confidants”), all of whom will be
informed of and be bound by this confidentiality provision. Neither Executive nor Executive’s Confidants shall disclose the fact, amount or terms of this Agreement to anyone including, but not limited to, any representative of any Internet,
print, radio or television media, to any past, present or prospective applicant for employment with the Company, executive recruiter or “headhunter,” to any counsel for any current or former employee of the Company, to any other counsel or
third party, or to the public at large. Executive understands and agrees that any disclosure of information in violation of this confidentiality provision by Executive or by any of Executive’s Confidants might cause the Company injury and
damage, the actual amount of which would be impractical or extremely difficult to determine, and therefore the Company may seek equitable relief. Otherwise, any alleged violation of this confidentiality provision shall be resolved in accordance with
the arbitration provisions herein. The Company shall have the burden of proving such violation by a preponderance of the evidence. 
 10. Governing Law. This Agreement shall be construed and enforced in accordance with, and the rights of the parties shall be governed by, the laws of the State of California or, where applicable,
United States federal law, in each case, without regard to any conflicts of laws provisions or those of any state other than California. 
 11. Miscellaneous. This Agreement, together with the Confidentiality Agreement and the Original Option Agreements, comprise the entire agreement between the parties with regard to the subject
matter hereof and supersedes, in their entirety, any other agreements between Executive and the Company with regard to the subject matter hereof, including, without limitation, the Offer Letter and Change of Control Agreement. Executive acknowledges
that there are no other agreements, written, oral or implied, and that he may not rely on any prior negotiations, discussions, representations or agreements. This Agreement may be modified only in writing, and such writing must be signed by both
parties and recited that it is intended to modify this Agreement. This Agreement may be executed in separate counterparts, each of which is deemed to be an original and all of which taken together constitute one and the same agreement. 

12. Executive’s Cooperation. Executive shall cooperate with the Company and its affiliates, upon the
Company’s reasonable request, with respect to any internal investigation or administrative, regulatory or judicial proceeding involving matters within the scope of Executive’s duties and responsibilities to the Company during his
employment with the Company (including, without limitation, Executive being available to the Company upon reasonable notice for interviews and factual investigations, appearing at the Company’s reasonable request to give testimony without
requiring service of a subpoena or other legal process, and turning over to the Company all relevant Company documents which are or may have come into Executive’s possession during his employment); provided, however, that any such
request by the Company shall not be unduly burdensome or interfere with Executive’s personal schedule or ability to engage in gainful employment.
  

 7 

 Confidential 
  

 13. Attorneys’ Fees. In the event that any dispute arises in
connection with this Agreement, or the Original Option Agreements, the prevailing party will be entitled to recover its reasonable costs and attorney fees, including reasonable expert witness fees. 
 (Signature Page Follows) 
  

 8 

 Confidential 
  

 IN WITNESS WHEREOF, the undersigned have caused this Separation Agreement to be duly
executed and delivered as of the date indicated next to their respective signatures below. 
  

							
	DATED: 6 AUG, 2009	 		 	
		 		 	 /s/ Robert S. Breuil

		 		 	Robert S. Breuil
			
		 		 	CODEXIS, INC.
	DATED: 6 August, 2009	 		 		 	
				
		 		 	By:	 	 /s/ Andy Danforth

		 		 		 	Andy Danforth
		 		 		 	V.P. Human Resources

  

 S-1 

 Confidential 
  

 EXHIBIT A 
 SUMMARY OF OUTSTANDING OPTIONS 
  

																	
	Option
Grant
Date	  	Option
Shares	  	VCD	  	Option
Expire
Date	  	Option
Exercise
price	  	Total
Option
Shares	  	Vested as of
June 30,
2009	  	Aggregate
Exercise
Price of
Vested
	1/3/2006	  	300,000	  	1/3/2006	  	1/2/2016	  	$	0.70	  	300,000	  	256,249	  	$	179,374.30
	1/26/2007	  	62,250	  	1/3/2006	  	1/25/2017	  	$	1.63	  	62,250	  	53,171	  	 	86,688.73
	1/26/2007	  	62,250	  	12/31/2006	  	1/25/2017	  	$	1.63	  	62,250	  	37,609	  	 	61,302.67
	8/28/2007	  	108,000	  	8/28/2007	  	8/27/2017	  	$	4.47	  	108,000	  	49,499	  	 	221,260.53
	10/25/2007	  	108,000	  	10/25/2007	  	10/24/2017	  	$	4.57	  	108,000	  	44,999	  	 	205,645.43
	6/9/2009	  	100,000	  	2/1/2009	  	6/2/2019	  	$	4.97	  	100,000	  	0	  	 	0.00
		  		  		  		  			  		  	 	  	 	 
		  		  		  		  			  	Total	  	441,527	  	$	754,251.66

  

 A-1

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