Document:

EX-10.3

 Exhibit 10.3 

PFENEX INC. 
 2014
EMPLOYEE STOCK PURCHASE PLAN 
 1. Purpose. The purpose of the Plan is to provide employees of the Company and its Designated
Companies with an opportunity to purchase Common Stock through accumulated Contributions. The Company intends for the Plan to have two components: a Code Section 423 Component (“423 Component”) and a non-Code Section 423
Component (“Non-423 Component”). The Company’s intention is to have the 423 Component of the Plan qualify as an “employee stock purchase plan” under Section 423 of the Code. The provisions of the 423 Component,
accordingly, will be construed so as to extend and limit Plan participation in a uniform and nondiscriminatory basis consistent with the requirements of Section 423 of the Code. In addition, this Plan authorizes the grant of an option to
purchase shares of Common Stock under the Non-423 Component that does not qualify as an “employee stock purchase plan” under Section 423 of the Code; such an option will be granted pursuant to rules, procedures or sub-plans adopted by
the Administrator designed to achieve tax, securities laws or other objectives for Eligible Employees and the Company. Except as otherwise provided herein, the Non-423 Component will operate and be administered in the same manner as the
423 Component. 
 2. Definitions. 

(a) “Administrator” means the Board or any Committee designated by the Board to administer the Plan pursuant to
Section 14. 
 (b) “Affiliate” means any entity, other than a Subsidiary, in which the Company has an equity or other
ownership interest. 
 (c) “Applicable Laws” means the requirements relating to the administration of equity-based awards
under U.S. state corporate laws, U.S. federal and state securities laws, the Code, any stock exchange or quotation system on which the Common Stock is listed or quoted and the applicable laws of any foreign country or jurisdiction where options are,
or will be, granted under the Plan. 
 (d) “Board” means the Board of Directors of the Company. 

(e) “Change in Control” means the occurrence of any of the following events: 

(i) A change in the ownership of the Company which occurs on the date that any one person, or more than one person acting as a group
(“Person”), acquires ownership of the stock of the Company that, together with the stock held by such Person, constitutes more than fifty percent (50%) of the total voting power of the stock of the Company; provided, however,
that for purposes of this subsection, the acquisition of additional stock by any one Person, who is considered to own more than fifty percent (50%) of the total voting power of the stock of the Company will not be considered a Change in
Control; or 

 (ii) A change in the effective control of the Company which occurs on the date that a majority
of members of the Board is replaced during any twelve (12) month period by Directors whose appointment or election is not endorsed by a majority of the members of the Board prior to the date of the appointment or election. For purposes of this
clause (ii), if any Person is considered to be in effective control of the Company, the acquisition of additional control of the Company by the same Person will not be considered a Change in Control; or 

(iii) A change in the ownership of a substantial portion of the Company’s assets which occurs on the date that any Person acquires (or
has acquired during the twelve (12) month period ending on the date of the most recent acquisition by such person or persons) assets from the Company that have a total gross fair market value equal to or more than fifty percent (50%) of
the total gross fair market value of all of the assets of the Company immediately prior to such acquisition or acquisitions; provided, however, that for purposes of this subsection, the following will not constitute a change in the ownership of a
substantial portion of the Company’s assets: (A) a transfer to an entity that is controlled by the Company’s stockholders immediately after the transfer, or (B) a transfer of assets by the Company to: (1) a stockholder of
the Company (immediately before the asset transfer) in exchange for or with respect to the Company’s stock, (2) an entity, fifty percent (50%) or more of the total value or voting power of which is owned, directly or indirectly, by
the Company, (3) a Person, that owns, directly or indirectly, fifty percent (50%) or more of the total value or voting power of all the outstanding stock of the Company, or (4) an entity, at least fifty percent (50%) of the total
value or voting power of which is owned, directly or indirectly, by a Person described in this subsection (iii)(B)(3). For purposes of this subsection, gross fair market value means the value of the assets of the Company, or the value of the assets
being disposed of, determined without regard to any liabilities associated with such assets. 
 For purposes of this definition, persons
will be considered to be acting as a group if they are owners of a corporation that enters into a merger, consolidation, purchase or acquisition of stock, or similar business transaction with the Company. 

Notwithstanding the foregoing, a transaction will not be deemed a Change in Control unless the transaction qualifies as a change in control
event within the meaning of Code Section 409A, as it has been and may be amended from time to time, and any proposed or final U.S. Treasury Regulations and Internal Revenue Service guidance that has been promulgated or may be promulgated
thereunder from time to time. 
 Further and for the avoidance of doubt, a transaction will not constitute a Change in Control if:
(i) its sole purpose is to change the state of the Company’s incorporation, or (ii) its sole purpose is to create a holding company that will be owned in substantially the same proportions by the persons who held the Company’s
securities immediately before such transaction. 
 (f) “Code” means the U.S. Internal Revenue Code of 1986, as amended.
Reference to a specific section of the Code or U.S. Treasury Regulation thereunder will include such section or regulation, any valid regulation or other official applicable guidance promulgated under such section, and any comparable provision of
any future legislation or regulation amending, supplementing or superseding such section or regulation. 

  
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 (g) “Committee” means a committee of the Board appointed in accordance with
Section 14 hereof. 
 (h) “Common Stock” means the common stock of the Company. 

(i) “Company” means Pfenex Inc., a Delaware corporation, or any successor thereto. 

(j) “Compensation” means an Eligible Employee’s base straight time gross earnings, but exclusive of payments for
incentive compensation, bonuses, payments for overtime and shift premium, equity compensation income and other similar compensation. The Administrator, in its discretion, may, on a uniform and nondiscriminatory basis, establish a different
definition of Compensation for a subsequent Offering Period. 
 (k) “Contributions” means the payroll deductions and other
additional payments that the Company may permit to be made by a Participant to fund the exercise of options granted pursuant to the Plan. 

(l) “Designated Company” means any Subsidiary or Affiliate that has been designated by the Administrator from time to time in
its sole discretion as eligible to participate in the Plan. For purposes of the 423 Component, only the Company and its Subsidiaries may be Designated Companies, provided, however that at any given time, a Subsidiary that is a Designated Company
under the 423 Component will not be a Designated Company under the Non-423 Component. 
 (m) “Director” means a member of
the Board. 
 (n) “Eligible Employee” means any individual who is a common law employee providing services to the Company
or a Designated Company and is customarily employed for at least twenty (20) hours per week and more than five (5) months in any calendar year by the Employer, or any lesser number of hours per week and/or number of months in any calendar
year established by the Administrator (if required under applicable local law) for purposes of any separate Offering or for Eligible Employees participating in the Non-423 Component. For purposes of the Plan, the employment relationship will be
treated as continuing intact while the individual is on sick leave or other leave of absence that the Employer approves or is legally protected under Applicable Laws. Where the period of leave exceeds three (3) months and the individual’s
right to reemployment is not guaranteed either by statute or by contract, the employment relationship will be deemed to have terminated three (3) months and one (1) day following the commencement of such leave. The Administrator, in its
discretion, from time to time may, prior to an Enrollment Date for all options to be granted on such Enrollment Date in an Offering, determine (on a uniform and nondiscriminatory basis or as otherwise permitted by Treasury Regulation Section 1.423-2) that the definition of Eligible Employee will or will not include an individual if he or she: (i) has not completed at least two (2) years of service since his or her last hire date
(or such lesser period of time as may be determined by the Administrator in its discretion), (ii) customarily works not more than twenty (20) hours per week (or such lesser period of time as may be determined by the Administrator in its
discretion), (iii) customarily works not more than five (5) months per calendar year (or such 

  
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lesser period of time as may be determined by the Administrator in its discretion), (iv) is a highly compensated employee within the meaning of Section 414(q) of the Code, or
(v) is a highly compensated employee within the meaning of Section 414(q) of the Code with compensation above a certain level or is an officer or subject to the disclosure requirements of Section 16(a) of the Exchange Act, provided
the exclusion is applied with respect to each Offering in an identical manner to all highly compensated individuals of the Employer whose Employees are participating in that Offering. Each exclusion will be applied with respect to an Offering in a
manner complying with U.S. Treasury Regulation Section 1.423-2(e)(2)(ii). 
 (o)
“Employer” means the employer of the applicable Eligible Employee(s). 
 (p) “Enrollment Date” means the
first Trading Day of each Offering Period. 
 (q) “Exchange Act” means the U.S. Securities Exchange Act of 1934, as
amended, including the rules and regulations promulgated thereunder. 
 (r) “Exercise Date” means the first Trading Day on
or after August 15 and February 15 of each Purchase Period. Notwithstanding the foregoing, the first Exercise Date under the Plan will be February 15, 2015. 

(s) “Fair Market Value” means, as of any date and unless the Administrator determines otherwise, the value of Common Stock
determined as follows: 
 (i) If the Common Stock is listed on any established stock exchange or a national market system, including without
limitation the New York Stock Exchange, NASDAQ Global Select Market, the NASDAQ Global Market or the NASDAQ Capital Market of The NASDAQ Stock Market, its Fair Market Value will be the closing sales price for such stock (or the closing bid, if no
sales were reported) as quoted on such exchange or system on the date of determination, as reported in The Wall Street Journal or such other source as the Administrator deems reliable; 

(ii) If the Common Stock is regularly quoted by a recognized securities dealer but selling prices are not reported, the Fair Market Value of
a Share will be the mean between the high bid and low asked prices for the Common Stock on the date of determination (or if no bids and asks were reported on that date, as applicable, on the last Trading Day such bids and asks were reported), as
reported in The Wall Street Journal or such other source as the Administrator deems reliable; 
 (iii) For purposes of the
Enrollment Date of the first Offering Period under the Plan, the Fair Market Value will be the initial price to the public as set forth in the final prospectus included within the registration statement on Form S-1 filed with the Securities and
Exchange Commission for the initial public offering of the Common Stock (the “Registration Statement”); or 
 (iv) In the
absence of an established market for the Common Stock, the Fair Market Value thereof will be determined in good faith by the Administrator. 

(t) “Fiscal Year” means the fiscal year of the Company. 

  
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 (u) “New Exercise Date” means a new Exercise Date if the Administrator shortens
any Offering Period then in progress. 
 (v) “Offering” means an offer under the Plan of an option that may be exercised
during an Offering Period as further described in Section 4. For purposes of the Plan, the Administrator may designate separate Offerings under the Plan (the terms of which need not be identical) in which Employees of one or more Employers will
participate, even if the dates of the applicable Offering Periods of each such Offering are identical and the provisions of the Plan will separately apply to each Offering. To the extent permitted by U.S. Treasury Regulation Section 1.423-2(a)(1), the terms of each Offering need not be identical provided that the terms of the Plan and an Offering together satisfy U.S. Treasury Regulation
Section 1.423-2(a)(2) and (a)(3). 
 (w) “Offering Periods” means the
periods of approximately twenty-four (24) months during which an option granted pursuant to the Plan may be exercised, (i) commencing on the first Trading Day on or after February 15 and August 15 of each year and terminating on
the first Trading Day on or after February 15 and August 15, approximately twenty-four (24) months later; provided, however, that the first Offering Period under the Plan will commence with the first Trading Day on or after the date
on which the Securities and Exchange Commission declares the Company’s Registration Statement effective and will end on the first Trading Day on or after August 15, 2016, and provided, further, that the second Offering Period under the
Plan will commence on the first Trading Day on or after February 15, 2015. The duration and timing of Offering Periods may be changed pursuant to Sections 4 and 20. 

(x) “Parent” means a “parent corporation,” whether now or hereafter existing, as defined in Section 424(e) of
the Code. 
 (y) “Participant” means an Eligible Employee that participates in the Plan. 

(z) “Plan” means this Pfenex Inc. 2014 Employee Stock Purchase Plan. 

(aa) “Purchase Period” means the approximately six (6) month period commencing after one Exercise Date and ending with
the next Exercise Date, except that the first Purchase Period of any Offering Period will commence on the Enrollment Date and end with the next Exercise Date. Unless the Administrator provides otherwise, the Purchase Period will have the same
duration and coincide with the length of the Offering Period. 
 (bb) “Purchase Price” means an amount equal to eighty-five
percent (85%) of the Fair Market Value of a share of Common Stock on the Enrollment Date or on the Exercise Date, whichever is lower; provided however, that the Purchase Price may be determined for subsequent Offering Periods by the
Administrator subject to compliance with Section 423 of the Code (or any successor rule or provision or any other Applicable Law, regulation or stock exchange rule) or pursuant to Section 20. 

(cc) “Registration Date” means the effective date of the first registration statement that is filed by the Company and
declared effective pursuant to Section 12(g) of the Exchange Act, with respect to any class of the Company’s securities. 

  
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 (dd) “Subsidiary” means a “subsidiary corporation,” whether now or
hereafter existing, as defined in Section 424(f) of the Code. 
 (ee) “Trading Day” means a day on which the national
stock exchange upon which the Common Stock is listed is open for trading. 
 (ff) “U.S. Treasury Regulations” means the
Treasury regulations of the Code. Reference to a specific Treasury Regulation or Section of the Code will include such Treasury Regulation or Section, any valid regulation promulgated under such Section, and any comparable provision of any future
legislation or regulation amending, supplementing or superseding such Section or regulation. 
 3. Eligibility. 

(a) First Offering Period. Any individual who is an Eligible Employee immediately prior to the first Offering Period will be
automatically enrolled in the first Offering Period. 
 (b) Subsequent Offering Periods. Any Eligible Employee on a given Enrollment
Date subsequent to the first Offering Period will be eligible to participate in the Plan, subject to the requirements of Section 5. 

(c) Non-U.S. Employees. Eligible Employees who are citizens or residents of a non-U.S. jurisdiction (without regard to whether they
also are citizens or residents of the United States or resident aliens (within the meaning of Section 7701(b)(1)(A) of the Code)) may be excluded from participation in the Plan or an Offering if the participation of such Eligible Employees is
prohibited under the laws of the applicable jurisdiction or if complying with the laws of the applicable jurisdiction would cause the Plan or an Offering to violate Section 423 of the Code. In the case of the Non-423 Component, Eligible
Employees may be excluded from participation in the Plan or an Offering if the Administrator has determined that participation of such Eligible Employees is not advisable or practicable. 

(d) Limitations. Any provisions of the Plan to the contrary notwithstanding, no Eligible Employee will be granted an option under the
Plan (i) to the extent that, immediately after the grant, such Eligible Employee (or any other person whose stock would be attributed to such Eligible Employee pursuant to Section 424(d) of the Code) would own capital stock of the Company
or any Parent or Subsidiary of the Company and/or hold outstanding options to purchase such stock possessing five percent (5%) or more of the total combined voting power or value of all classes of the capital stock of the Company or of any
Parent or Subsidiary of the Company, or (ii) to the extent that his or her rights to purchase stock under all employee stock purchase plans (as defined in Section 423 of the Code) of the Company or any Parent or Subsidiary of the Company
accrues at a rate, which exceeds twenty-five thousand dollars ($25,000) worth of stock (determined at the Fair Market Value of the stock at the time such option is granted) for each calendar year in which such option is outstanding at any time, as
determined in accordance with Section 423 of the Code and the regulations thereunder. 
 4. Offering Periods. The Plan will be
implemented by consecutive Offering Periods with a new Offering Period commencing on the first Trading Day on or after February 15 and 

  
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August 15 each year, or on such other date as the Administrator will determine; provided, however, that the first Offering Period under the Plan will commence with the first Trading Day on
or after the date upon which the Company’s Registration Statement is declared effective by the Securities and Exchange Commission and end on the first Trading Day on or after August 15, 2016, and provided, further, that the second Offering
Period under the Plan will commence on the first Trading Day on or after February 15, 2015. The Administrator will have the power to change the duration of Offering Periods (including the commencement dates thereof) with respect to future
Offerings without stockholder approval if such change is announced prior to the scheduled beginning of the first Offering Period to be affected thereafter; provided, however, that no Offering Period may last more than twenty-seven (27) months.

 5. Participation. 

(a) First Offering Period. An Eligible Employee will be entitled to continue to participate in the first Offering Period pursuant to
Section 3(a) only if such individual submits a subscription agreement authorizing Contributions in a form determined by the Administrator (which may be similar to the form attached hereto as Exhibit A) to the Company’s designated
plan administrator (i) no earlier than the effective date of the Form S-8 registration statement with respect to the issuance of Common Stock under this Plan and (ii) no later than ten (10) business days following the effective date
of such S-8 registration statement or such other period of time as the Administrator may determine (the “Enrollment Window”). An Eligible Employee’s failure to submit the subscription agreement during the Enrollment Window will
result in the automatic termination of such individual’s participation in the first Offering Period. 
 (b) Subsequent Offering
Periods. An Eligible Employee may participate in the Plan pursuant to Section 3(b) by (i) submitting to the Company’s stock administration office (or its designee), on or before a date determined by the Administrator prior to an
applicable Enrollment Date, a properly completed subscription agreement authorizing Contributions in the form provided by the Administrator for such purpose, or (ii) following an electronic or other enrollment procedure determined by the
Administrator. 
 6. Contributions. 

(a) At the time a Participant enrolls in the Plan pursuant to Section 5, he or she will elect to have Contributions (in the form of
payroll deductions or otherwise, to the extent permitted by the Administrator) made on each pay day during the Offering Period in an amount not exceeding fifteen percent (15%) of the Compensation, which he or she receives on each pay day during
the Offering Period (for illustrative purposes, should a pay day occur on an Exercise Date, a Participant will have any payroll deductions made on such day applied to his or her account under the then-current Purchase Period or Offering Period). The
Administrator, in its sole discretion, may permit all Participants in a specified Offering to contribute amounts to the Plan through payment by cash, check or other means set forth in the subscription agreement prior to each Exercise Date of each
Purchase Period. A Participant’s subscription agreement will remain in effect for successive Offering Periods unless terminated as provided in Section 10 hereof. 

  
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 (b) In the event Contributions are made in the form of payroll deductions, such payroll
deductions for a Participant will commence on the first pay day following the Enrollment Date and will end on the last pay day prior to the Exercise Date of such Offering Period to which such authorization is applicable, unless sooner terminated by
the Participant as provided in Section 10 hereof; provided, however, that for the first Offering Period, payroll deductions will commence on the first pay day on or following the end of the Enrollment Window. 

(c) All Contributions made for a Participant will be credited to his or her account under the Plan and Contributions will be made in whole
percentages only. A Participant may not make any additional payments into such account. 
 (d) A Participant may discontinue his or her
participation in the Plan as provided in Section 10. Except as may be permitted by the Administrator, as determined in its sole discretion, a Participant may not change the rate of his or her Contributions during an Offering Period. 

(e) Notwithstanding the foregoing, to the extent necessary to comply with Section 423(b)(8) of the Code and Section 3(d), a
Participant’s Contributions may be decreased to zero percent (0%) at any time during a Purchase Period. Subject to Section 423(b)(8) of the Code and Section 3(d) hereof, Contributions will recommence at the rate originally elected by
the Participant effective as of the beginning of the first Purchase Period scheduled to end in the following calendar year, unless terminated by the Participant as provided in Section 10. 

(f) Notwithstanding any provisions to the contrary in the Plan, the Administrator may allow Eligible Employees to participate in the Plan via
cash contributions instead of payroll deductions if (i) payroll deductions are not permitted under applicable local law, (ii) the Administrator determines that cash contributions are permissible under Section 423 of the Code or
(iii) for Participants participating in the Non-423 Component. 
 (g) At the time the option is exercised, in whole or in part, or at
the time some or all of the Common Stock issued under the Plan is disposed of (or any other time that a taxable event related to the Plan occurs), the Participant must make adequate provision for the Company’s or Employer’s federal, state,
local or any other tax liability payable to any authority including taxes imposed by jurisdictions outside of the U.S., national insurance, social security or other tax withholding obligations, if any, which arise upon the exercise of the option or
the disposition of the Common Stock (or any other time that a taxable event related to the Plan occurs). At any time, the Company or the Employer may, but will not be obligated to, withhold from the Participant’s compensation the amount
necessary for the Company or the Employer to meet applicable withholding obligations, including any withholding required to make available to the Company or the Employer any tax deductions or benefits attributable to sale or early disposition of
Common Stock by the Eligible Employee. In addition, the Company or the Employer may, but will not be obligated to, withhold from the proceeds of the sale of Common Stock or any other method of withholding the Company or the Employer deems
appropriate to the extent permitted by U.S. Treasury Regulation Section 1.423-2(f). 

  
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 7. Grant of Option. On the Enrollment Date of each Offering Period, each Eligible Employee
participating in such Offering Period will be granted an option to purchase on each Exercise Date during such Offering Period (at the applicable Purchase Price) up to a number of shares of Common Stock determined by dividing such Eligible
Employee’s Contributions accumulated prior to such Exercise Date and retained in the Eligible Employee’s account as of the Exercise Date by the applicable Purchase Price; provided that in no event will an Eligible Employee be permitted to
purchase during each Purchase Period more than 700 shares of Common Stock (subject to any adjustment pursuant to Section 19) and provided further that such purchase will be subject to the limitations set forth in Sections 3(d) and 13. The
Eligible Employee may accept the grant of such option (i) with respect to the first Offering Period by submitting a properly completed subscription agreement in accordance with the requirements of Section 5 on or before the last day of the
Enrollment Window, and (ii) with respect to any subsequent Offering Period under the Plan, by electing to participate in the Plan in accordance with the requirements of Section 5. The Administrator may, for future Offering Periods,
increase or decrease, in its absolute discretion, the maximum number of shares of Common Stock that an Eligible Employee may purchase during each Purchase Period of an Offering Period. Exercise of the option will occur as provided in Section 8,
unless the Participant has withdrawn pursuant to Section 10. The option will expire on the last day of the Offering Period. 
 8.
Exercise of Option. 
 (a) Unless a Participant withdraws from the Plan as provided in Section 10, his or her option for the
purchase of shares of Common Stock will be exercised automatically on the Exercise Date, and the maximum number of full shares subject to the option will be purchased for such Participant at the applicable Purchase Price with the accumulated
Contributions from his or her account. No fractional shares of Common Stock will be purchased; any Contributions accumulated in a Participant’s account, which are not sufficient to purchase a full share will be retained in the
Participant’s account for the subsequent Purchase Period or Offering Period, subject to earlier withdrawal by the Participant as provided in Section 10. Any other funds left over in a Participant’s account after the Exercise Date will
be returned to the Participant. During a Participant’s lifetime, a Participant’s option to purchase shares hereunder is exercisable only by him or her. 

(b) If the Administrator determines that, on a given Exercise Date, the number of shares of Common Stock with respect to which options are to
be exercised may exceed (i) the number of shares of Common Stock that were available for sale under the Plan on the Enrollment Date of the applicable Offering Period, or (ii) the number of shares of Common Stock available for sale under
the Plan on such Exercise Date, the Administrator may in its sole discretion (x) provide that the Company will make a pro rata allocation of the shares of Common Stock available for purchase on such Enrollment Date or Exercise Date, as
applicable, in as uniform a manner as will be practicable and as it will determine in its sole discretion to be equitable among all Participants exercising options to purchase Common Stock on such Exercise Date, and continue all Offering Periods
then in effect or (y) provide that the Company will make a pro rata allocation of the shares available for purchase on such Enrollment Date or Exercise Date, as applicable, in as uniform a manner as will be practicable and as it will determine
in its sole discretion to be equitable among all participants exercising options to purchase Common Stock on such Exercise Date, and terminate any or all Offering Periods then in effect pursuant to 

  
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Section 20. The Company may make a pro rata allocation of the shares available on the Enrollment Date of any applicable Offering Period pursuant to the preceding sentence, notwithstanding
any authorization of additional shares for issuance under the Plan by the Company’s stockholders subsequent to such Enrollment Date. 

9. Delivery. As soon as reasonably practicable after each Exercise Date on which a purchase of shares of Common Stock occurs, the
Company will arrange the delivery to each Participant of the shares purchased upon exercise of his or her option in a form determined by the Administrator (in its sole discretion) and pursuant to rules established by the Administrator. The Company
may permit or require that shares be deposited directly with a broker designated by the Company or to a designated agent of the Company, and the Company may utilize electronic or automated methods of share transfer. The Company may require that
shares be retained with such broker or agent for a designated period of time and/or may establish other procedures to permit tracking of disqualifying dispositions of such shares. No Participant will have any voting, dividend, or other stockholder
rights with respect to shares of Common Stock subject to any option granted under the Plan until such shares have been purchased and delivered to the Participant as provided in this Section 9. 

10. Withdrawal. 
 (a) A
Participant may withdraw all but not less than all the Contributions credited to his or her account and not yet used to exercise his or her option under the Plan at any time by (i) submitting to the Company’s stock administration office
(or its designee) a written notice of withdrawal in the form determined by the Administrator for such purpose (which may be similar to the form attached hereto as Exhibit B), or (ii) following an electronic or other withdrawal procedure
determined by the Administrator. All of the Participant’s Contributions credited to his or her account will be paid to such Participant promptly after receipt of notice of withdrawal and such Participant’s option for the Offering Period
will be automatically terminated, and no further Contributions for the purchase of shares will be made for such Offering Period. If a Participant withdraws from an Offering Period, Contributions will not resume at the beginning of the succeeding
Offering Period, unless the Participant re-enrolls in the Plan in accordance with the provisions of Section 5. 
 (b) A
Participant’s withdrawal from an Offering Period will not have any effect upon his or her eligibility to participate in any similar plan that may hereafter be adopted by the Company or in succeeding Offering Periods that commence after the
termination of the Offering Period from which the Participant withdraws. 
 11. Termination of Employment. Upon a Participant’s
ceasing to be an Eligible Employee for any reason, he or she will be deemed to have elected to withdraw from the Plan and the Contributions credited to such Participant’s account during the Offering Period but not yet used to purchase shares of
Common Stock under the Plan will be returned to such Participant or, in the case of his or her death, to the person or persons entitled thereto under Section 15, and such Participant’s option will be automatically terminated. A Participant
whose employment transfers between entities through a termination with an immediate rehire (with no break in 

  
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service) by the Company or a Designated Company will not be treated as terminated under the Plan; however, if a Participant transfers from an Offering under the 423 Component to the Non-423
Component, the exercise of the option will be qualified under the 423 Component only to the extent it complies with Section 423 of the Code. 

12. Interest. No interest will accrue on the Contributions of a participant in the Plan, except as may be required by Applicable Law,
as determined by the Company, and if so required by the laws of a particular jurisdiction, will apply to all Participants in the relevant Offering under the 423 Component, except to the extent otherwise permitted by U.S. Treasury Regulation Section 1.423-2(f). 
 13. Stock. 

(a) Subject to adjustment upon changes in capitalization of the Company as provided in Section 19 hereof, the maximum number of shares of
Common Stock that will be made available for sale under the Plan will be 355,618 shares of Common Stock. The number of shares of Common Stock available for issuance under the Plan will be increased on the first day of each Fiscal Year beginning
with the 2015 Fiscal Year equal to the least of (i) 355,618 shares of Common Stock, (ii) one and one-half percent (1.5%) of the outstanding shares of Common Stock on the last day of the immediately preceding Fiscal Year, or
(iii) an amount determined by the Administrator. 
 (b) Until the shares of Common Stock are issued (as evidenced by the appropriate
entry on the books of the Company or of a duly authorized transfer agent of the Company), a Participant will have only the rights of an unsecured creditor with respect to such shares, and no right to vote or receive dividends or any other rights as
a stockholder will exist with respect to such shares. 
 (c) Shares of Common Stock to be delivered to a Participant under the Plan will be
registered in the name of the Participant or in the name of the Participant and his or her spouse. 
 14. Administration. The Plan
will be administered by the Board or a Committee appointed by the Board, which Committee will be constituted to comply with Applicable Laws. The Administrator will have full and exclusive discretionary authority to construe, interpret and apply the
terms of the Plan, to designate separate Offerings under the Plan, to designate Subsidiaries and Affiliates as participating in the 423 Component or Non-423 Component, to determine eligibility, to adjudicate all disputed claims filed under the Plan
and to establish such procedures that it deems necessary for the administration of the Plan (including, without limitation, to adopt such procedures and sub-plans as are necessary or appropriate to permit the participation in the Plan by employees
who are foreign nationals or employed outside the U.S., the terms of which sub-plans may take precedence over other provisions of this Plan, with the exception of Section 13(a) hereof, but unless otherwise superseded by the terms of such
sub-plan, the provisions of this Plan will govern the operation of such sub-plan). Unless otherwise determined by the Administrator, the Employees eligible to participate in each sub-plan will participate in a separate Offering or in the Non-423
Component. Without limiting the generality of the foregoing, the Administrator is specifically authorized to adopt rules and procedures 

  
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regarding eligibility to participate, the definition of Compensation, handling of Contributions, making of Contributions to the Plan (including, without limitation, in forms other than payroll
deductions), establishment of bank or trust accounts to hold Contributions, payment of interest, conversion of local currency, obligations to pay payroll tax, determination of beneficiary designation requirements, withholding procedures and handling
of stock certificates that vary with applicable local requirements. The Administrator also is authorized to determine that, to the extent permitted by U.S. Treasury Regulation Section 1.423-2(f), the
terms of an option granted under the Plan or an Offering to citizens or residents of a non-U.S. jurisdiction will be less favorable than the terms of options granted under the Plan or the same Offering to employees resident solely in the U.S. Every
finding, decision and determination made by the Administrator will, to the full extent permitted by law, be final and binding upon all parties. 

15. Designation of Beneficiary. 

(a) If permitted by the Administrator, a Participant may file a designation of a beneficiary who is to receive any shares of Common Stock and
cash, if any, from the Participant’s account under the Plan in the event of such Participant’s death subsequent to an Exercise Date on which the option is exercised but prior to delivery to such Participant of such shares and cash. In
addition, if permitted by the Administrator, a Participant may file a designation of a beneficiary who is to receive any cash from the Participant’s account under the Plan in the event of such Participant’s death prior to exercise of the
option. If a Participant is married and the designated beneficiary is not the spouse, spousal consent will be required for such designation to be effective. 

(b) Such designation of beneficiary may be changed by the Participant at any time by notice in a form determined by the Administrator. In the
event of the death of a Participant and in the absence of a beneficiary validly designated under the Plan who is living at the time of such Participant’s death, the Company will deliver such shares and/or cash to the executor or administrator
of the estate of the Participant, or if no such executor or administrator has been appointed (to the knowledge of the Company), the Company, in its discretion, may deliver such shares and/or cash to the spouse or to any one or more dependents or
relatives of the Participant, or if no spouse, dependent or relative is known to the Company, then to such other person as the Company may designate. 

(c) All beneficiary designations will be in such form and manner as the Administrator may designate from time to time. Notwithstanding
Sections 15(a) and (b) above, the Company and/or the Administrator may decide not to permit such designations by Participants in non-U.S. jurisdictions to the extent permitted by U.S. Treasury Regulation
Section 1.423-2(f). 
 16. Transferability. Neither Contributions credited to a
Participant’s account nor any rights with regard to the exercise of an option or to receive shares of Common Stock under the Plan may be assigned, transferred, pledged or otherwise disposed of in any way (other than by will, the laws of descent
and distribution or as provided in Section 15 hereof) by the Participant. Any such attempt at assignment, transfer, pledge or other disposition will be without effect, except that the Company may treat such act as an election to withdraw funds
from an Offering Period in accordance with Section 10 hereof. 

  
 - 12 - 

 17. Use of Funds. The Company may use all Contributions received or held by it under the
Plan for any corporate purpose, and the Company will not be obligated to segregate such Contributions except under Offerings or for Participants in the Non-423 Component for which Applicable Laws require that Contributions to the Plan by
Participants be segregated from the Company’s general corporate funds and/or deposited with an independent third party. Until shares of Common Stock are issued, Participants will have only the rights of an unsecured creditor with respect to
such shares. 
 18. Reports. Individual accounts will be maintained for each Participant in the Plan. Statements of account will be
given to participating Eligible Employees at least annually, which statements will set forth the amounts of Contributions, the Purchase Price, the number of shares of Common Stock purchased and the remaining cash balance, if any. 

19. Adjustments, Dissolution, Liquidation, Merger or Change in Control. 

(a) Adjustments. In the event that any dividend or other distribution (whether in the form of cash, Common Stock, other securities, or
other property), recapitalization, stock split, reverse stock split, reorganization, merger, consolidation, split-up, spin-off, combination, repurchase, or exchange of Common Stock or other securities of the Company, or other change in the corporate
structure of the Company affecting the Common Stock occurs, the Administrator, in order to prevent dilution or enlargement of the benefits or potential benefits intended to be made available under the Plan, will, in such manner as it may deem
equitable, adjust the number and class of Common Stock that may be delivered under the Plan, the Purchase Price per share and the number of shares of Common Stock covered by each option under the Plan that has not yet been exercised, and the
numerical limits of Sections 7 and 13. 
 (b) Dissolution or Liquidation. In the event of the proposed dissolution or liquidation of
the Company, any Offering Period then in progress will be shortened by setting a New Exercise Date, and will terminate immediately prior to the consummation of such proposed dissolution or liquidation, unless provided otherwise by the Administrator.
The New Exercise Date will be before the date of the Company’s proposed dissolution or liquidation. The Administrator will notify each Participant in writing or electronically, prior to the New Exercise Date, that the Exercise Date for the
Participant’s option has been changed to the New Exercise Date and that the Participant’s option will be exercised automatically on the New Exercise Date, unless prior to such date the Participant has withdrawn from the Offering Period as
provided in Section 10 hereof. 
 (c) Merger or Change in Control. In the event of a merger or Change in Control, each
outstanding option will be assumed or an equivalent option substituted by the successor corporation or a Parent or Subsidiary of the successor corporation. In the event that the successor corporation refuses to assume or substitute for the option,
the Offering Period with respect to which such option relates will be shortened by setting a New Exercise Date on which such Offering Period will end. The New Exercise Date will occur before the date of the Company’s proposed merger or Change
in Control. The Administrator will notify each Participant in writing or electronically prior to the New Exercise Date, that the Exercise Date for the Participant’s option has been changed to the New Exercise Date and that the
Participant’s 

  
 - 13 - 

 
option will be exercised automatically on the New Exercise Date, unless prior to such date the Participant has withdrawn from the Offering Period as provided in Section 10 hereof. 

20. Amendment or Termination. 

(a) The Administrator, in its sole discretion, may amend, suspend, or terminate the Plan, or any part thereof, at any time and for any reason.
If the Plan is terminated, the Administrator, in its discretion, may elect to terminate all outstanding Offering Periods either immediately or upon completion of the purchase of shares of Common Stock on the next Exercise Date (which may be sooner
than originally scheduled, if determined by the Administrator in its discretion), or may elect to permit Offering Periods to expire in accordance with their terms (and subject to any adjustment pursuant to Section 19). If the Offering Periods
are terminated prior to expiration, all amounts then credited to Participants’ accounts that have not been used to purchase shares of Common Stock will be returned to the Participants (without interest thereon, except as otherwise
required under Applicable Laws, as further set forth in Section 12 hereof) as soon as administratively practicable. 
 (b) Without
stockholder consent and without limiting Section 20(a), the Administrator will be entitled to change the Offering Periods or Purchase Periods, designate separate Offerings, limit the frequency and/or number of changes in the amount withheld
during an Offering Period, establish the exchange ratio applicable to amounts withheld in a currency other than U.S. dollars, permit Contributions in excess of the amount designated by a Participant in order to adjust for delays or mistakes in the
Company’s processing of properly completed Contribution elections, establish reasonable waiting and adjustment periods and/or accounting and crediting procedures to ensure that amounts applied toward the purchase of Common Stock for each
Participant properly correspond with Contribution amounts, and establish such other limitations or procedures as the Administrator determines in its sole discretion advisable that are consistent with the Plan. 

(c) In the event the Administrator determines that the ongoing operation of the Plan may result in unfavorable financial accounting
consequences, the Administrator may, in its discretion and, to the extent necessary or desirable, modify, amend or terminate the Plan to reduce or eliminate such accounting consequence including, but not limited to: 

(i) amending the Plan to conform with the safe harbor definition under the Financial Accounting Standards Board Accounting Standards
Codification Topic 718 (or any successor thereto), including with respect to an Offering Period underway at the time; 
 (ii) altering the
Purchase Price for any Offering Period or Purchase Period including an Offering Period or Purchase Period underway at the time of the change in Purchase Price; 

(iii) shortening any Offering Period or Purchase Period by setting a New Exercise Date, including an Offering Period or Purchase Period
underway at the time of the Administrator action; 
 (iv) reducing the maximum percentage of Compensation a Participant may elect to set
aside as Contributions; and 

  
 - 14 - 

 (v) reducing the maximum number of Shares a Participant may purchase during any Offering Period
or Purchase Period. 
 Such modifications or amendments will not require stockholder approval or the consent of any Participants. 

21. Notices. All notices or other communications by a Participant to the Company under or in connection with the Plan will be deemed to
have been duly given when received in the form and manner specified by the Company at the location, or by the person, designated by the Company for the receipt thereof. 

22. Conditions Upon Issuance of Shares. Shares of Common Stock will not be issued with respect to an option unless the exercise of such
option and the issuance and delivery of such shares pursuant thereto will comply with all applicable provisions of law, domestic or foreign, including, without limitation, the U.S. Securities Act of 1933, as amended, the Exchange Act, the rules and
regulations promulgated thereunder, and the requirements of any stock exchange upon which the shares may then be listed, and will be further subject to the approval of counsel for the Company with respect to such compliance. 

As a condition to the exercise of an option, the Company may require the person exercising such option to represent and warrant at the time of
any such exercise that the shares are being purchased only for investment and without any present intention to sell or distribute such shares if, in the opinion of counsel for the Company, such a representation is required by any of the
aforementioned applicable provisions of law. 
 23. Code Section 409A. The 423 Component of the Plan is exempt from the
application of Code Section 409A and any ambiguities herein will be interpreted to so be exempt from Code Section 409A. In furtherance of the foregoing and notwithstanding any provision in the Plan to the contrary, if the Administrator
determines that an option granted under the Plan may be subject to Code Section 409A or that any provision in the Plan would cause an option under the Plan to be subject to Code Section 409A, the Administrator may amend the terms of the
Plan and/or of an outstanding option granted under the Plan, or take such other action the Administrator determines is necessary or appropriate, in each case, without the Participant’s consent, to exempt any outstanding option or future option
that may be granted under the Plan from or to allow any such options to comply with Code Section 409A, but only to the extent any such amendments or action by the Administrator would not violate Code Section 409A. Notwithstanding the
foregoing, the Company will have no liability to a Participant or any other party if the option to purchase Common Stock under the Plan that is intended to be exempt from or compliant with Code Section 409A is not so exempt or compliant or for
any action taken by the Administrator with respect thereto. The Company makes no representation that the option to purchase Common Stock under the Plan is compliant with Code Section 409A. 

24. Term of Plan. The Plan will become effective upon the earlier to occur of its adoption by the Board or its approval by the
stockholders of the Company. It will continue in effect for a term of twenty (20) years, unless sooner terminated under Section 20. 

  
 - 15 - 

 25. Stockholder Approval. The Plan will be subject to approval by the stockholders of the
Company within twelve (12) months after the date the Plan is adopted by the Board. Such stockholder approval will be obtained in the manner and to the degree required under Applicable Laws. 

26. Governing Law. The Plan will be governed by, and construed in accordance with, the laws of the State of California (except its
choice-of-law provisions). 
 27. No Right to Employment. Participation in the Plan by a Participant will not be construed as giving
a Participant the right to be retained as an employee of the Company or a Subsidiary or Affiliate, as applicable. Furthermore, the Company or a Subsidiary or Affiliate may dismiss a Participant from employment at any time, free from any liability or
any claim under the Plan. 
 28. Severability. If any provision of the Plan is or becomes or is deemed to be invalid, illegal, or
unenforceable for any reason in any jurisdiction or as to any Participant, such invalidity, illegality or unenforceability will not affect the remaining parts of the Plan, and the Plan will be construed and enforced as to such jurisdiction or
Participant as if the invalid, illegal or unenforceable provision had not been included. 
 29. Compliance with Applicable Laws. The
terms of this Plan are intended to comply with all Applicable Laws and will be construed accordingly. 

  
 - 16 - 

 EXHIBIT A 

PFENEX INC. 
 2014
EMPLOYEE STOCK PURCHASE PLAN 
 SUBSCRIPTION AGREEMENT 

 

			
	Original Application	  	Offering Date:                    
	Change in Payroll Deduction Rate	  	

 1.
                    hereby elects to participate in the Pfenex Inc. 2014 Employee Stock Purchase Plan (the “Plan”) and subscribes to
purchase shares of the Company’s Common Stock in accordance with this Subscription Agreement and the Plan. 
 2. I hereby authorize
payroll deductions from each paycheck in the amount of     % of my Compensation on each payday (from 0 to 15%) during the Offering Period in accordance with the Plan. (Please note that no fractional percentages are permitted.)

 3. I understand that said payroll deductions will be accumulated for the purchase of shares of Common Stock at the applicable Purchase
Price determined in accordance with the Plan. I understand that if I do not withdraw from an Offering Period, any accumulated payroll deductions will be used to automatically exercise my option and purchase Common Stock under the Plan. 

4. I have received a copy of the complete Plan and its accompanying prospectus. I understand that my participation in the Plan is in all
respects subject to the terms of the Plan. 
 5. Shares of Common Stock purchased for me under the Plan should be issued in the name(s) of
                    (Eligible Employee or Eligible Employee and Spouse only). 

6. I understand that if I dispose of any shares received by me pursuant to the Plan within two (2) years after the Offering Date (the
first day of the Offering Period during which I purchased such shares) or one (1) year after the Exercise Date, I will be treated for federal income tax purposes as having received ordinary income at the time of such disposition in an amount
equal to the excess of the fair market value of the shares at the time such shares were purchased by me over the price that I paid for the shares. I hereby agree to notify the Company in writing within thirty (30) days after the date of any
disposition of my shares and I will make adequate provision for federal, state or other tax withholding obligations, if any, which arise upon the disposition of the Common Stock. The Company may, but will not be obligated to, withhold from my
compensation the amount necessary to meet any applicable withholding obligation including any withholding necessary to make available to the Company any tax deductions or benefits attributable to sale or early disposition of Common Stock by me. If I
dispose of such shares at any time after the expiration of the two (2) year and one (1) year holding periods, I understand that I will be treated for federal income tax purposes as having 

  
 - 17 - 

 
received income only at the time of such disposition, and that such income will be taxed as ordinary income only to the extent of an amount equal to the lesser of (a) the excess of the fair
market value of the shares at the time of such disposition over the purchase price which I paid for the shares, or (b) 15% of the fair market value of the shares on the first day of the Offering Period. The remainder of the gain, if any,
recognized on such disposition will be taxed as capital gain. 
 7. I hereby agree to be bound by the terms of the Plan. The effectiveness
of this Subscription Agreement is dependent upon my eligibility to participate in the Plan. 
  

					
	 Employee’s Social

Security Number:
	  		  	 
			
	 Employee’s Address:
	  		  	 
			
		  		  	 
			
		  		  	 

 I UNDERSTAND THAT THIS SUBSCRIPTION AGREEMENT WILL REMAIN IN EFFECT THROUGHOUT SUCCESSIVE OFFERING PERIODS
UNLESS TERMINATED BY ME. 
  

							
	 Dated:
	  	 	  		 	  

		  		  		 	Signature of Employee    

  
 - 18 - 

 EXHIBIT B 

PFENEX INC. 
 2014
EMPLOYEE STOCK PURCHASE PLAN 
 NOTICE OF WITHDRAWAL 

The undersigned Participant in the Offering Period of the Pfenex Inc. 2014 Employee Stock Purchase Plan that began on
                    ,             (the “Offering Date”) hereby notifies
the Company that he or she hereby withdraws from the Offering Period. He or she hereby directs the Company to pay to the undersigned as promptly as practicable all the payroll deductions credited to his or her account with respect to such Offering
Period. The undersigned understands and agrees that his or her option for such Offering Period will be terminated automatically. The undersigned understands further that no further payroll deductions will be made for the purchase of shares in the
current Offering Period and the undersigned will be eligible to participate in succeeding Offering Periods only by delivering to the Company a new Subscription Agreement. 

 

	
	 Name and Address of Participant:

	
	 
	
	 
	
	 
	
	 Signature:

	
	 

 
			
		
	 Date:
	 	 

  
 - 19 -EX-10.14

 Exhibit 10.14 

CREDIT AGREEMENT 
 THIS CREDIT
AGREEMENT (this “Agreement”) is entered into as of May 1, 2012, by and between PFENEX INC,, a Delaware corporation (“Borrower”), and WELLS FARGO BANK, NATIONAL ASSOCIATION (“Bank”). 

RECITALS 
 Borrower has
requested that Bank extend or continue credit to Borrower as described below, and Bank has agreed to provide such credit to Borrower on the terms and conditions contained herein. 

NOW, THEREFORE, for valuable consideration, the receipt and sufficiency of which are hereby acknowledged, Bank and Borrower hereby agree as
follows: 
 ARTICLE I 

CREDIT TERMS 

SECTION 1.1. LINE OF CREDIT. 

(a) Line of Credit. Subject to the terms and conditions of this Agreement, Bank hereby agrees to make advances to Borrower from time to
time up to and including April 2, 2015, not to exceed at any time the aggregate principal amount of One Million Five Hundred Thousand Dollars ($1,500,000.00) (“Line of Credit”), the proceeds of which shall be used to finance
Borrower’s working capital requirements. Borrower’s obligation to repay advances under the Line of Credit shall be evidenced by a promissory note dated as of May 1, 2012 (“Line of Credit Note”), all terms of which are
incorporated herein by this reference. 
 (b) Borrowing and Repayment. Borrower may from time to time during the term of the Line of
Credit borrow, partially or wholly repay its outstanding borrowings, and reborrow, subject to all of the limitations, terms and conditions contained herein or in the Line of Credit Note; provided however, that the total outstanding borrowings under
the Line of Credit shall not at any time exceed the maximum principal amount available thereunder, as set forth above. 
 SECTION 1.2.
INTEREST/FEES. 
 (a) Interest. The outstanding principal balance of each credit subject hereto shall bear Interest at the rate of
interest set forth in each promissory note or other instrument or document executed in connection therewith. 
 (b) Computation and
Payment. Interest shall be computed on the basis of a 360-day year, actual days elapsed. Interest shall be payable at the times and place set forth in each promissory note or other instrument or document required hereby. 

SECTION 1.3. COLLATERAL. 

As security for all indebtedness and other obligations of Borrower to Bank subject hereto, Borrower hereby grants to Bank security interests
of first priority in all Borrower’s funds deposited in Borrower’s Money Market Account #[*]. All of the foregoing shall be evidenced by and subject to the terms of such security agreements, financing statements, deeds or mortgages, and
other documents as Bank shall reasonably require, all in form and substance satisfactory to Bank. Borrower shall pay to Bank immediately upon demand the full amount of all charges, costs and expenses (to include fees paid to third parties and all
allocated costs of Bank personnel), expended or incurred by Bank in connection with any of the foregoing security, including without limitation, filing and recording fees and costs of appraisals, audits and title insurance. 

 ARTICLE II 

REPRESENTATIONS AND WARRANTIES 

Borrower makes the following representations and warranties to Bank, which representations and warranties shall survive the execution of this
Agreement and shall continue in full force and effect until the full and final payment, and satisfaction and discharge, of all obligations of Borrower to Bank subject to this Agreement. 

SECTION 2.1. LEGAL STATUS. Borrower is a corporation, duly organized and existing and in good standing under the laws of Delaware, and is
qualified or licensed to do business (and is in good standing as a foreign corporation, if applicable) in all jurisdictions in which such qualification or licensing is required or in which the failure to so qualify or to be so licensed could have a
material adverse effect on Borrower. 
 SECTION 2.2. AUTHORIZATION AND VALIDITY. This Agreement and each promissory note, contract,
instrument and other document required hereby or at any time hereafter delivered to Bank in connection herewith (collectively, the “Loan Documents”) have been duly authorized, and upon their execution and delivery in accordance with the
provisions hereof will constitute legal, valid and binding agreements and obligations of Borrower or the party which executes the same, enforceable in accordance with their respective terms. 

SECTION 2.3. NO VIOLATION. The execution, delivery and performance by Borrower of each of the Loan Documents do not violate any provision
of any law or regulation, or contravene any provision of the Articles of Incorporation or By-Laws of Borrower, or result in any breach of or default under any contract, obligation, indenture or other instrument to which Borrower is a party or by
which Borrower may be bound. 
 SECTION 2.4. LITIGATION. There are no pending, or to the best of Borrower’s knowledge threatened,
actions, claims, investigations, suits or proceedings by or before any governmental authority, arbitrator, court or administrative agency which could have a material adverse effect on the financial condition or operation of Borrower other than those
disclosed by Borrower to Bank in writing prior to the date hereof. 
 SECTION 2.5. CORRECTNESS OF FINANCIAL STATEMENT. The annual
financial statement of Borrower dated December 31, 2010, and all interim financial statements delivered to Bank since said date, true copies of which have been delivered by Borrower to Bank prior to the date hereof, (a) are complete and
correct and present fairly the financial condition of Borrower, (b) disclose all liabilities of Borrower that are required to be reflected or reserved against under generally accepted accounting principles, whether liquidated or unliquidated,
fixed or contingent, and (c) have been prepared in accordance with generally accepted accounting principles consistently applied. Since the dates of such financial statements there has been no material adverse change in the financial condition
of Borrower, nor has Borrower mortgaged, pledged, granted a security interest in or otherwise encumbered any of its assets or properties except in favor of Bank or as otherwise permitted by Bank in writing. 

SECTION 2.6. INCOME TAX RETURNS. Borrower has no knowledge of any pending assessments or adjustments of its income tax payable with
respect to any year. 
 SECTION 2.7. NO SUBORDINATION. There is no agreement, indenture, contract or instrument to which Borrower is a
party or by which Borrower may be bound that requires the subordination in right of payment of any of Borrower’s obligations subject to this Agreement to any other obligation of Borrower. 

SECTION 2.8. PERMITS, FRANCHISES. Borrower possesses, and will hereafter possess, all permits, consents, approvals, franchises and
licenses required and rights to all trademarks, trade names, patents, and fictitious names, if any, necessary to enable it to conduct the business in which it is now engaged in compliance with applicable law. 

  
 -2- 

 SECTION 2.9. ERISA. Borrower is in compliance in all material respects with all applicable
provisions of the Employee Retirement Income Security Act of 1974, as amended or recodified from time to time (“ERISA”); Borrower has not violated any provision of any defined employee pension benefit plan (as defined in ERISA) maintained
or contributed to by Borrower (each, a “Plan”); no Reportable Event as defined in ERISA has occurred and is continuing with respect to any Plan initiated by Borrower; Borrower has met its minimum funding requirements under ERISA with
respect to each Plan; and each Plan will be able to fulfill its benefit obligations as they come due in accordance with the Plan documents and under generally accepted accounting principles. 

SECTION 2.10. OTHER OBLIGATIONS. Borrower is not in default on any obligation for borrowed money, any purchase money obligation or any
other material lease, commitment, contract, Instrument or obligation. 
 SECTION 2.11. ENVIRONMENTAL MATTERS. Except as disclosed by
Borrower to Bank in writing prior to the date hereof, Borrower is in compliance in all material respects with all applicable federal or state environmental, hazardous waste, health and safety statutes, and any rules or regulations adopted pursuant
thereto, which govern or affect any of Borrower’s operations and/or properties, including without limitation, the Comprehensive Environmental Response, Compensation and Liability Act of 1980, the Superfund Amendments and Reauthorization Act of
1986, the Federal Resource Conservation and Recovery Act of 1976, and the Federal Toxic Substances Control Act, as any of the same may be amended, modified or supplemented from time to time. None of the operations of Borrower is the subject of any
federal or state investigation evaluating whether any remedial action involving a material expenditure is needed to respond to a release of any toxic or hazardous waste or substance into the environment. Borrower has no material contingent liability
in connection with any release of any toxic or hazardous waste or substance into the environment. 
 ARTICLE III 

CONDITIONS 

SECTION 3.1. CONDITIONS OF INITIAL EXTENSION OF CREDIT. The obligation of Bank to extend any credit contemplated by this Agreement Is
subject to the fulfillment to Bank’s satisfaction of all of the following conditions: 
 (a) Approval of Bank Counsel. All legal
matters incidental to the extension of credit by Bank shall be satisfactory to Bank’s counsel. 
 (b) Documentation. Bank shall
have received, in form and substance satisfactory to Bank, each of the following, duty executed: 
  

	 	(i)	This Agreement and each promissory note or other instrument or document required hereby. 

  

	 	(ii)	Corporate Resolution: Borrowing. 

  

	 	(iii)	Certificate of Incumbency. 

  

	 	(iv)	Security Agreement: Specific Rights to Payment. 

  

	 	(v)	Such other documents as Bank may require under any other Section of this Agreement. 

 (c)
Financial Condition. There shall have been no material adverse change, as determined by Bank, in the financial condition or business of Borrower, nor any material decline, as determined by Bank, in the market value of any collateral required
hereunder or a substantial or material portion of the assets of Borrower. 
 (d) Insurance. Borrower shall have delivered to Bank
evidence of insurance coverage on all Borrower’s property, in form, substance, amounts, covering risks and issued by companies satisfactory to Bank, and where required by Bank, with loss payable endorsements in favor of Bank. 

  
 -3- 

 SECTION 3.2. CONDITIONS OF EACH EXTENSION OF CREDIT. The obligation of Bank to make each
extension of credit requested by Borrower hereunder shall be subject to the fulfillment to Bank’s satisfaction of each of the following conditions: 

(a) Compliance. The representations and warranties contained herein and in each of the other Loan Documents shall be true on and as of
the date of the signing of this Agreement and on the date of each extension of credit by Bank pursuant hereto, with the same effect as though such representations and warranties had been made on and as of each such date, and on each such date, no
Event of Default as defined herein, and no condition, event or act which with the giving of notice or the passage of time or both would constitute such an Event of Default, shall have occurred and be continuing or shall exist. 

(b) Documentation. Bank shall have received all additional documents which may be required in connection with such extension of credit.

 ARTICLE IV 

AFFIRMATIVE COVENANTS 

Borrower covenants that so long as Bank remains committed to extend credit to Borrower pursuant hereto, or any liabilities (whether direct or
contingent, liquidated or unliquidated) of Borrower to Bank under any of the Loan Documents remain outstanding, and until payment in full of all obligations of Borrower subject hereto, Borrower shall, unless Bank otherwise consents in writing: 

SECTION 4.1. PUNCTUAL PAYMENTS. Punctually pay all principal, interest, fees or other liabilities due under any of the Loan Documents at
the times and place and in the manner specified therein. 
 SECTION 4.2. ACCOUNTING RECORDS. Maintain adequate books and records in
accordance with generally accepted accounting principles consistently applied, and permit any representative of Bank, at any reasonable time, to inspect, audit and examine such books and records, to make copies of the same, and to inspect the
properties of Borrower. 
 SECTION 4.3. FINANCIAL STATEMENTS. Provide to Bank all of the following, in form and detail satisfactory to
Bank: 
 (a) not later than 90 days after and as of the end of each fiscal year, a compiled financial statement of Borrower, prepared by a
certified public accountant acceptable to Bank, to include balance sheet, income statement and statement of cash flows; 
 (b) not later
than 45 days after and as of the end of each fiscal quarter, a financial statement of Borrower, prepared by Borrower, to include balance sheet and income statement; 

(c) from time to time such other information as Bank may reasonably request. 

SECTION 4.4. COMPLIANCE. Preserve and maintain all licenses, permits, governmental approvals, rights, privileges and franchises necessary
for the conduct of its business; and comply with the provisions of all documents pursuant to which Borrower is organized and/or which govern Borrower’s continued existence and with the requirements of all laws, rules, regulations and orders of
any governmental authority applicable to Borrower and/or its business. 
 SECTION 4.5. INSURANCE. Maintain and keep in force, for each
business in which Borrower is engaged, insurance of the types and in amounts customarily carried in similar lines of business, including but 

  
 -4- 

 
not limited to fire, extended coverage, public liability, flood, property damage and workers’ compensation, with all such insurance carried with companies and in amounts satisfactory to
Bank, and deliver to Bank from time to time at Bank’s request schedules setting forth all insurance then in effect. 

SECTION 4.6. FACILITIES. Keep all properties useful or necessary to Borrower’s business in good repair and condition, and from time
to time make necessary repairs, renewals and replacements thereto so that such properties shall be fully and efficiently preserved and maintained. 

SECTION 4.7. TAXES AND OTHER LIABILITIES. Pay and discharge when due any and all indebtedness, obligations, assessments and taxes, both
real or personal, including without limitation federal and state income taxes and state and local property taxes and assessments, except (a) such as Borrower may in good faith contest or as to which a bona fide dispute may arise, and
(b) for which Borrower has made provision, to Bank’s satisfaction, for eventual payment thereof in the event Borrower is obligated to make such payment. 

SECTION 4.8. LITIGATION. Promptly give notice in writing to Bank of any litigation pending or threatened against Borrower. 

SECTION 4.9. NOTICE TO BANK. Promptly (but in no event more than five (5) days after the occurrence of each such event or matter)
give written notice to Bank in reasonable detail of: (a) the occurrence of any Event of Default, or any condition, event or act which with the giving of notice or the passage of time or both would constitute an Event of Default; (b) any
change in the name or the organizational structure of Borrower; (c) the occurrence and nature of any Reportable Event or Prohibited Transaction, each as defined in ERISA, or any funding deficiency with respect to any Plan; or (d) any
termination or cancellation of any insurance policy which Borrower is required to maintain, or any uninsured or partially uninsured loss through liability or property damage, or through fire, theft or any other cause affecting Borrower’s
property. 
 ARTICLE V 

NEGATIVE COVENANTS 

Borrower further covenants that so long as Bank remains committed to extend credit to Borrower pursuant hereto, or any liabilities (whether
direct or contingent, liquidated or unliquidated) of Borrower to Bank under any of the Loan Documents remain outstanding, and until payment in full of all obligations of Borrower subject hereto, Borrower will not without Bank’s prior written
consent: 
 SECTION 5.1. USE OF FUNDS. Use any of the proceeds of any credit extended hereunder except for the purposes stated in
Article I hereof. 
 SECTION 5.2. CAPITAL EXPENDITURES. Make any additional investment in fixed assets in any fiscal year. 

SECTION 5.3. LEASE EXPENDITURES. Incur operating lease expense in any fiscal year. 

SECTION 5.4. OTHER INDEBTEDNESS. Create, incur, assume or permit to exist any indebtedness or liabilities resulting from borrowings,
loans or advances, whether secured or unsecured, matured or unmatured, liquidated or unliquidated, joint or several, except (a) the liabilities of Borrower to Bank, and (b) any other liabilities of Borrower existing as of, and disclosed to
Bank prior to, the date hereof. 
 SECTION 5.5. MERGER, CONSOLIDATION, TRANSFER OF ASSETS. Merge into or consolidate with any other
entity; make any substantial change in the nature of Borrower’s business as conducted as of the date hereof; acquire all or substantially all of the assets of any other entity; nor sell, lease, transfer or otherwise dispose of all or a
substantial or material portion of Borrower’s assets except in the ordinary course of its business. 

  
 -5- 

 SECTION 5.6. GUARANTIES. Guarantee or become liable in any way as surety, endorser (other
than as endorser of negotiable instruments for deposit or collection in the ordinary course of business), accommodation endorser or otherwise for, nor pledge or hypothecate any assets of Borrower as security for, any liabilities or obligations of
any other person or entity, except any of the foregoing in favor of Bank. 
 SECTION 5.7. LOANS, ADVANCES, INVESTMENTS. Make any loans
or advances to or investments in any person or entity, except any of the foregoing existing as of, and disclosed to Bank prior to, the date hereof. 

SECTION 5.8. DIVIDENDS, DISTRIBUTIONS. Declare or pay any dividend or distribution either in cash, stock or any other property on
Borrower’s stock now or hereafter outstanding, nor redeem, retire, repurchase or otherwise acquire any shares of any class of Borrower’s stock now or hereafter outstanding. 

SECTION 5.9. PLEDGE OF ASSETS. Mortgage, pledge, grant or permit to exist a security interest in, or lien upon, all or any portion of
Borrower’s assets now owned or hereafter acquired, except any of the foregoing in favor of Bank or which is existing as of, and disclosed to Bank in writing prior to, the date hereof. 

ARTICLE VI 
 EVENTS
OF DEFAULT 
 SECTION 6.1. The occurrence of any of the following shall constitute an “Event of Default” under this
Agreement: 
 (a) Borrower shall fail to pay when due any principal, interest, fees or other amounts payable under any of the Loan
Documents. 
 (b) Any financial statement or certificate furnished to Bank in connection with, or any representation or warranty made by
Borrower or any other party under this Agreement or any other Loan Document shall prove to be incorrect, false or misleading in any material respect when furnished or made. 

(c) Any default in the performance of or compliance with any obligation, agreement or other provision contained herein or in any other Loan
Document (other than those specifically described as an “Event of Default” in this section 6.1), and with respect to any such default that by its nature can be cured, such default shall continue for a period of twenty (20) days from
the earlier of (1) the date an executive officer of Borrower learns of such default, or (2) the date written notice thereof is given by Bank to Borrower. 

(d) Any default in the payment or performance of any obligation, or any defined event of default, under the terms of any contract, instrument
or document (other than any of the Loan Documents) pursuant to which Borrower, any guarantor hereunder or any general partner or joint venturer in Borrower if a partnership or joint venture (with each such guarantor, general partner and/or joint
venturer referred to herein as a “Third Party Obligor”) has incurred any debt or other liability to any person or entity, including Bank; provided however, that any cure period applicable thereto has expired, and in the case of a default
or defined event of default to a person or entity other than Bank or an affiliate of Bank, (1) such indebtedness is in excess of $50,000.00, individually or in the aggregate for all such defaults by Borrower and each Third Party Obligor
combined, and (2) such default or defined event of default is not being contested in good faith by Borrower or such Third Party Obligor, as the case may be, or, if being so contested, they have not made provision to Bank’s reasonable
satisfaction for payment thereof in the event they were to lose such contest. 
 (e) Borrower or any Third Party Obligor shall become
insolvent, or shall suffer or consent to or apply for the appointment of a receiver, trustee, custodian or liquidator of itself or any of its property, or shall generally fail to pay its debts as they become due, or shall make a general assignment
for the benefit of creditors; Borrower or any Third Party Obligor shall file a voluntary petition in bankruptcy, or seeking reorganization, in order to effect a plan or other arrangement with creditors or any other relief under the Bankruptcy Reform
Act, Title 11 of the United States Code, as amended or recodified from time to time 

  
 -6- 

 
(“Bankruptcy Code”), or under any state or federal law granting relief to debtors, whether now or hereafter in effect; or Borrower or any Third Party Obligor shall file an answer
admitting the jurisdiction of the court and the material allegations of any involuntary petition; or Borrower or any Third Party Obligor shall be adjudicated a bankrupt, or an order for relief shall be entered against Borrower or any Third Party
Obligor by any court of competent Jurisdiction under the Bankruptcy Code or any other applicable state or federal law relating to bankruptcy, reorganization or other relief for debtors. 

(f) The filing of a notice of judgment lien against Borrower or any Third Party Obligor; or the recording of any abstract of judgment against
Borrower or any Third Party Obligor in any county in which Borrower or such Third Party Obligor has an interest in real property; or the service of a notice of levy and/or of a writ of attachment or execution, or other like process, against the
assets of Borrower or any Third Party Obligor; or the entry of a judgment against Borrower or any Third Party Obligor; provided, however, that such judgments, liens, levies, writs, executions and other process involve debts of or claims against
Borrower or any Third Party Obligor in excess of $50,000.00, individually or in the aggregate for all such judgments, liens, levies, writs, executions and other process combined, and within thirty (20 days after the creation thereof, or at least ten
(10) days prior to the date on which any assets could be lawfully sold in satisfaction thereof, such debt or claim is not satisfied or stayed pending appeal and insured against in a manner satisfactory to Bank; or any involuntary petition or
proceeding pursuant to the Bankruptcy Code or any other applicable state or federal law relating to bankruptcy, reorganization or other relief for debtors is filed or commenced against Borrower or any Third Party Obligor. 

(g) There shall exist or occur any event or condition that Bank in good faith believes impairs, or is substantially likely to impair, the
prospect of payment or performance by Borrower, any Third Party Obligor, or the general partner of either if such entity is a partnership, of its obligations under any of the Loan Documents, and such event or condition is not cured to the reasonable
satisfaction of Bank within thirty (30) days after Bank gives Borrower written notice thereof. 
 (h) The death or incapacity of
Borrower or any Third Party Obligor if an individual. The dissolution or liquidation of Borrower or any Third Party Obligor if a corporation, partnership, joint venture or other type of entity; or Borrower or any such Third Party Obligor, or any of
its directors, stockholders or members, shall take action seeking to effect the dissolution or liquidation of Borrower or such Third Party Obligor. 

(i) Any change in control of Borrower or any entity or combination of entities that directly or indirectly control Borrower, with
“control” defined as ownership of an aggregate of twenty-five percent (25%) or more of the common stock, members’ equity or other ownership interest (other than a limited partnership interest). 

SECTION 6.2. REMEDIES. Upon the occurrence of any Event of Default: (a) all indebtedness of Borrower under each of the Loan
Documents, any term thereof to the contrary notwithstanding, shall at Bank’s option and without notice become immediately due and payable without presentment, demand, protest or notice of dishonor, all of which are hereby expressly waived by
Borrower; (b) the obligation, if any, of Bank to extend any further credit under any of the Loan Documents shall immediately cease and terminate; and (c) Bank shall have all rights, powers and remedies available under each of the Loan
Documents, or accorded by law, including without limitation the right to resort to any or all security for any credit subject hereto and to exercise any or all of the rights of a beneficiary or secured party pursuant to applicable law. All rights,
powers and remedies of Bank may be exercised at any time by Bank and from time to time after the occurrence of an Event of Default, are cumulative and not exclusive, and shall be in addition to any other rights, powers or remedies provided by law or
equity. 

  
 -7- 

 ARTICLE VII 

MISCELLANEOUS 

SECTION 7.1. NO WAIVER. No delay, failure or discontinuance of Bank in exercising any right, power or remedy under any of the Loan
Documents shall affect or operate as a waiver of such right, power or remedy; nor shall any single or partial exercise of any such right, power or remedy preclude, waive or otherwise affect any other or further exercise thereof or the exercise of
any other right, power or remedy. Any waiver, permit, consent or approval of any kind by Bank of any breach of or default under any of the Loan Documents must be in writing and shall be effective only to the extent set forth in such writing. 

SECTION 7.2. NOTICES. All notices, requests and demands which any party is required or may desire to give to any other party under any
provision of this Agreement must be in writing delivered to each party at the following address: 
  

			
	BORROWER:	  	PFENEX INC.
		  	10790 Roselle Street
		  	San Diego, CA 92121
		
	BANK:	  	WELLS FARGO BANK, NATIONAL ASSOCIATION
		  	San Diego RCBO
		  	401 B Street, Suite 2201
		  	San Diego, CA 92101

 or to such other address as any party may designate by written notice to all other parties. Each such notice, request and
demand shall be deemed given or made as follows: (a) if sent by hand delivery, upon delivery; (b) if sent by mail, upon the earlier of the date of receipt or three (3) days after deposit in the U.S. mail, first class and postage
prepaid; and (c) if sent by telecopy, upon receipt. 
 SECTION 7.3. COSTS, EXPENSES AND ATTORNEYS’ FEES. Borrower shall pay
to Bank within twenty (20) days of written demand by Bank (which demand shall include a reasonably detailed summary of the amounts which are the subject thereof) the full amount of all reasonable payments, advances, charges, costs and expenses,
including reasonable attorneys’ fees (excluding allocated costs of Bank’s in-house counsel), expended or incurred by Bank in connection with (a) the preparation of any amendments and waivers to this Agreement and the other Loan
Documents, (b) the enforcement of Bank’s rights and/or the collection of any amounts which become due to Bank under any of the Loan Documents, and (c) the prosecution or defense of any action in any way related to any of the Loan
Documents, Including without limitation, any action for declaratory relief, whether incurred at the trial or appellate level, in an arbitration proceeding or otherwise, and including any of the foregoing incurred in connection with any bankruptcy
proceeding (including without limitation, any adversary proceeding, contested matter or motion brought by Bank or any other person) relating to Borrower or any other party to any of the Loan Documents. Notwithstanding anything herein to the
contrary, the prevailing party in any action to enforce this Agreement or any of the other Loan Documents shall be entitled to recover from the non-prevailing party in such action all reasonable costs and expenses, including without limitation
reasonable attorneys’ fees, expended or incurred by the prevailing party in such action. 
 SECTION 7.4. SUCCESSORS, ASSIGNMENT.
This Agreement shall be binding upon and inure to the benefit of the heirs, executors, administrators, legal representatives, successors and assigns of the parties; provided however, that Borrower may not assign or transfer its interests or rights
hereunder without Bank’s prior written consent. Bank reserves the right to sell, assign, transfer, negotiate or grant participations in all or any part of, or any interest in, Bank’s rights and benefits under each of the Loan Documents. In
connection therewith, Bank may disclose all documents and information which Bank now has or may hereafter acquire relating to any credit subject hereto, Borrower or its business, or any collateral required hereunder. 

SECTION 7.5. ENTIRE AGREEMENT; AMENDMENT. This Agreement and the other Loan Documents constitute the entire agreement between Borrower
and Bank with respect to each credit subject hereto and supersede all prior negotiations, communications, discussions and correspondence concerning the subject matter hereof. This Agreement may be amended or modified only in writing signed by each
party hereto. 

  
 -8- 

 SECTION 7.6. NO THIRD PARTY BENEFICIARIES, This Agreement is made and entered into for the
sole protection and benefit of the parties hereto and their respective permitted successors and assigns, and no other person or entity shall be a third party beneficiary of, or have any direct or indirect cause of action or claim in connection with,
this Agreement or any other of the Loan Documents to which it is not a party. 
 SECTION 7.7. TIME. Time is of the essence of each and
every provision of this Agreement and each other of the Loan Documents. 
 SECTION 7.8. SEVERABILITY OF PROVISIONS. If any provision of
this Agreement shall be prohibited by or invalid under applicable law, such provision shall be ineffective only to the extent of such prohibition or invalidity without invalidating the remainder of such provision or any remaining provisions of this
Agreement. 
 SECTION 7.9. COUNTERPARTS. This Agreement may be executed in any number of counterparts, each of which when executed and
delivered shall be deemed to be an original, and all of which when taken together shall constitute one and the same Agreement. 

SECTION 7.10. GOVERNING LAW. This Agreement shall be governed by and construed in accordance with the laws of the State of California.

 SECTION 7.11. ARBITRATION. 

(a) Arbitration. The parties hereto agree, upon demand by any party, to submit to binding arbitration all claims, disputes and
controversies between or among them (and their respective employees, officers, directors, attorneys, and other agents), whether in tort, contract or otherwise in any way arising out of or relating to (i) any credit subject hereto, or any of the
Loan Documents, and their negotiation, execution, collateralization, administration, repayment, modification, extension, substitution, formation, inducement, enforcement, default or termination; or (ii) requests for additional credit. 

(b) Governing Rules. Any arbitration proceeding will (i) proceed in a location in California selected by the American Arbitration
Association (“AAA”); (ii) be governed by the Federal Arbitration Act (Title 9 of the United States Code), notwithstanding any conflicting choice of law provision in any of the documents between the parties; and (iii) be
conducted by the AAA, or such other administrator as the parties shall mutually agree upon, in accordance with the AAA’s commercial dispute resolution procedures, unless the claim or counterclaim is at least $1,000,000.00 exclusive of claimed
interest, arbitration fees and costs in which case the arbitration shall be conducted in accordance with the AAA’s optional procedures for large, complex commercial disputes (the commercial dispute resolution procedures or the optional
procedures for large, complex commercial disputes to be referred to herein, as applicable, as the “Rules”). If there is any inconsistency between the terms hereof and the Rules, the terms and procedures set forth herein shall control. Any
party who fails or refuses to submit to arbitration following a demand by any other party shall bear all costs and expenses incurred by such other party in compelling arbitration of any dispute. Nothing contained herein shall be deemed to be a
waiver by any party that is a bank of the protections afforded to it under 12 U.S.C. §91 or any similar applicable state law. 
 (c)
No Waiver of Provisional Remedies, Self-Help and Foreclosure. The arbitration requirement does not limit the right of any party to (i) foreclose against real or personal property collateral; (ii) exercise self-help remedies relating
to collateral or proceeds of collateral such as setoff or repossession; or (iii) obtain provisional or ancillary remedies such as replevin, injunctive relief, attachment or the appointment of a receiver, before during or after the pendency of
any arbitration proceeding. This exclusion does not constitute a waiver of the right or obligation of any party to submit any dispute to arbitration or reference hereunder, including those arising from the exercise of the actions detailed in
sections (i), (ii) and (iii) of this paragraph. 

  
 -9- 

 (d) Arbitrator Qualifications and Powers. Any arbitration proceeding in which the amount
in controversy is $5,000,000.00 or less will be decided by a single arbitrator selected according to the Rules, and who shall not render an award of greater than $5,000,000.00. Any dispute in which the amount in controversy exceeds $5,000,000.00
shall be decided by majority vote of a panel of three arbitrators; provided however, that all three arbitrators must actively participate in all hearings and deliberations. The arbitrator will be a neutral attorney licensed in the State of
California or a neutral retired judge of the state or federal judiciary of California, in either case with a minimum of ten years experience in the substantive law applicable to the subject matter of the dispute to be arbitrated. The arbitrator will
determine whether or not an issue Is arbitratable and will give effect to the statutes of limitation in determining any claim. In any arbitration proceeding the arbitrator will decide (by documents only or with a hearing at the arbitrator’s
discretion) any pre-hearing motions which are similar to motions to dismiss for failure to state a claim or motions for summary adjudication. The arbitrator shall resolve all disputes in accordance with the substantive law of California and may
grant any remedy or relief that a court of such state could order or grant within the scope hereof and such ancillary relief as is necessary to make effective any award. The arbitrator shall also have the power to award recovery of all costs and
fees, to impose sanctions and to take such other action as the arbitrator deems necessary to the same extent a judge could pursuant to the Federal Rules of Civil Procedure, the California Rules of Civil Procedure or other applicable law. Judgment
upon the award rendered by the arbitrator may be entered in any court having jurisdiction. The institution and maintenance of an action for judicial relief or pursuit of a provisional or ancillary remedy shall not constitute a waiver of the right of
any party, including the plaintiff, to submit the controversy or claim to arbitration if any other party contests such action for judicial relief. 

(e) Discovery. In any arbitration proceeding, discovery will be permitted in accordance with the Rules. All discovery shall be
expressly limited to matters directly relevant to the dispute being arbitrated and must be completed no later than 20 days before the hearing date. Any requests for an extension of the discovery periods, or any discovery disputes, will be subject to
final determination by the arbitrator upon a showing that the request for discovery is essential for the party’s presentation and that no alternative means for obtaining information is available. 

(f) Class Proceedings and Consolidations. No party hereto shall be entitled to join or consolidate disputes by or against others in any
arbitration, except parties who have executed any Loan Document, or to include in any arbitration any dispute as a representative or member of a class, or to act in any arbitration in the interest of the general public or in a private attorney
general capacity. 
 (g) Payment Of Arbitration Costs And Fees. The arbitrator shall award all costs and expenses of the arbitration
proceeding. 
 (h) Real Property Collateral; Judicial Reference. Notwithstanding anything herein to the contrary, no dispute shall be
submitted to arbitration if the dispute concerns indebtedness secured directly or indirectly, In whole or in part, by any real property unless (i) the holder of the mortgage, lien or security interest specifically elects in writing to proceed
with the arbitration, or (Ii) all parties to the arbitration waive any rights or benefits that might accrue to them by virtue of the single action rule statute of California, thereby agreeing that all indebtedness and obligations of the parties, and
all mortgages, liens and security interests securing such indebtedness and obligations, shall remain fully valid and enforceable. If any such dispute is not submitted to arbitration, the dispute shall be referred to a referee in accordance with
California Code of Civil Procedure Section 638 et seq., and this general reference agreement is intended to be specifically enforceable in accordance with said Section 638. A referee with the qualifications required herein for arbitrators
shall be selected pursuant to the AAA’s selection procedures. Judgment upon the decision rendered by a referee shall be entered in the court in which such proceeding was commenced in accordance with California Code of Civil Procedure
Sections 644 and 645. 
 (i) Miscellaneous. To the maximum extent practicable, the AAA, the arbitrators and the parties shall
take all action required to conclude any arbitration proceeding within 180 days of the filing of the dispute with the AAA. No arbitrator or other party to an arbitration proceeding may disclose the existence, content or

  
 -10- 

 
results thereof, except for disclosures of information by a party required in the ordinary course of its business or by applicable law or regulation. If more than one agreement for arbitration by
or between the parties potentially applies to a dispute, the arbitration provision most directly related to the Loan Documents or the subject matter of the dispute shall control. This arbitration provision shall survive termination, amendment or
expiration of any of the Loan Documents or any relationship between the parties. 
 (j) Small Claims Court. Notwithstanding anything
herein to the contrary, each party retains the right to pursue in Small Claims Court any dispute within that court’s jurisdiction. Further, this arbitration provision shall apply only to disputes in which either party seeks to recover an amount
of money (excluding attorneys’ fees and costs) that exceeds the jurisdictional limit of the Small Claims Court. 
 IN WITNESS WHEREOF,
the parties hereto have caused this Agreement to be executed as of the day and year first written above. 
  

									
	PFENEX INC.	 		 	WELLS FARGO BANK, NATIONAL ASSOCIATION
					
	By:	 	 /s/ Bertrand Liang
	 		 	By:	 	 /s/ Linda K. Schneider

	Title:	 	CEO	 		 		 	 Linda K. Schneider,
 Relationship
Manager

  
 -11- 

			
	WELLS FARGO	  	CERTIFICATE OF INCUMBENCY

  
 TO: WELLS FARGO
BANK, NATIONAL ASSOCIATION (“Bank”) 
 The undersigned, Bertrand Liang, Secretary of PFENEX INC., a corporation created and
existing under the laws of Delaware, hereby certifies to Bank that: (a) the following named persons are duly elected officers of this corporation and presently hold the titles specified below; (b) said officers are authorized to act
on behalf of this Corporation in transactions with Bank; and (c) the signature opposite each officer’s name is his or her true signature: 
  

					
	TITLE	  	NAME	 	SIGNATURE
			
	Chief Executive Officer	  	Bertrand Liang	 	 /s/ Bertrand Liang

 The undersigned further certifies that if any of the above-named officers change, or if, at any time, any of
said officers are no longer authorized to act on behalf of this corporation in transactions with Bank, this corporation shall immediately provide to Bank a new Certificate of Incumbency. Bank is hereby authorized to rely on this Certificate of
Incumbency until a new Certificate of Incumbency certified by the Secretary of this corporation is received by Bank. 
 IN TESTIMONY
WHEREOF, I have hereunto set my hand, and if required by Bank affixed the corporate seal of said corporation, as of May 17, 2012. 
  

	
	 /s/ Bertrand Liang

	Secretary

 (SEAL) 

			
	WELLS FARGO	  	CORPORATE RESOLUTION: BORROWING

  
 TO: WELLS FARGO
BANK, NATIONAL ASSOCIATION (“Bank”) 
 RESOLVED: That this corporation, PFENEX INC., proposes to obtain credit from time to
time, or has obtained credit, from Bank. 
 BE IT FURTHER RESOLVED, that any one of the following officers (use titles only): 

Chief Executive Officer 
 of this
corporation be and they are hereby authorized and empowered for and on behalf of and in the name of this corporation and as its corporate act and deed: 

(a) To borrow money from Bank and to assume any liabilities of any other person or entity to Bank, in such form and on such terms and
conditions as shall be agreed upon by those authorized above and Bank, and to sign and deliver to Bank such promissory notes and other evidences of indebtedness for money borrowed or advanced and/or for indebtedness assumed as Bank shall require;
such promissory notes or other evidences of indebtedness may provide that advances be requested by telephone communication and by any officer, employee or agent of this corporation so long as the advances are deposited into any deposit account of
this corporation with Bank; this corporation shall be bound to Bank by, and Bank may rely upon, any communication or act, including telephone communications, purporting to be done by any officer, employee or agent of this corporation provided that
Bank believes, in good faith, that the same is done by such person. 
 (b) To contract for the issuance by Bank of letters of credit, to
discount with Bank notes, acceptances and evidences of indebtedness payable to or due this corporation, to endorse the same and execute such contracts and instruments for repayment thereof to Bank as Bank shall require, and to enter into any swap,
derivative, foreign exchange, hedge or other similar transaction or arrangement with or through Bank. 
 (c) To mortgage, encumber, pledge,
convey, grant, assign or otherwise transfer all or any part of this corporation’s real or personal property for the purpose of securing the payment of any of the promissory notes, contracts, instruments and other evidences of indebtedness
authorized hereby, and to execute and deliver to Bank such deeds of trust, mortgages, pledge agreements, security agreements and/or other related documents as Bank shall require. 

(d) To perform all acts and to execute and deliver all documents described above and all other contracts and instruments which Bank deems
necessary or convenient to accomplish the purposes of this resolution and/or to perfect or continue the rights, remedies and security interests to be given to Bank pursuant hereto, including without limitation, any modifications, renewals and/or
extensions of any of this corporation’s obligations to Bank, however evidenced; provided that the aggregate principal amount of all sums borrowed and credits established pursuant to this resolution shall not at any time exceed the sum of
$1,500,000.00 outstanding and unpaid. 
 Loans made pursuant to a special resolution and loans made by offices of Bank other than the office
to which this resolution is delivered shall be in addition to foregoing limitation. 
 BE IT FURTHER RESOLVED, that the authority hereby
conferred is in addition to that conferred by any other resolution heretofore or hereafter delivered by this corporation to Bank and shall continue in full force and effect until Bank shall have received notice in writing, certified by the Secretary
of this corporation, of the revocation hereof by a resolution duly adopted by the Board of Directors of this corporation. Any such revocation shall be effective only as to credit which is extended or committed by Bank, or actions which are taken by
this corporation pursuant to the resolutions contained herein, subsequent to Bank’s receipt of such notice. The authority hereby conferred shall be deemed retroactive, and any and all acts authorized herein which were performed prior to the
passage of this resolution are hereby approved and ratified. 
 SEE FOLLOWING PAGE FOR CERTIFICATION 

 CERTIFICATION 

I, Bertrand Liang, Secretary of PFENEX INC., a corporation created and existing under the laws of Delaware, do hereby certify
and declare that the foregoing is a full, true and correct copy of the resolutions duly passed and adopted by the Board of Directors of said corporation, by written consent of all Directors of said corporation or at a meeting of said Board duly and
regularly called, noticed and held on May 17, 2012, at which meeting a quorum of the Board of Directors was present and voted in favor of said resolutions; that said resolutions are now in full force and effect; that there is no provision in
the Articles of Incorporation or Bylaws of said corporation, or any shareholder agreement, limiting the power of the Board of Directors of said corporation to pass the foregoing resolutions and that such resolutions are in conformity with the
provisions of such Articles of Incorporation and Bylaws; and that no approval by the shareholders of, or of the outstanding shares of, said corporation is required with respect to the matters which are the subject of the foregoing resolutions. 

IN WITNESS WHEREOF, I have hereunto set my hand, and if required by Bank affixed the corporate seal of said corporation, as of May 17,
2012 
  

	
	/s/ Bertrand Liang, Secretary

 (SEAL) 

 FIRST AMENDMENT TO CREDIT AGREEMENT 

THIS AMENDMENT TO CREDIT AGREEMENT (this “Amendment”) is entered into as of June 24, 2013, by and between PFENEX INC., a
Delaware corporation (“Borrower”), and WELLS FARGO BANK, NATIONAL ASSOCIATION (“Bank”). 
 RECITALS 

WHEREAS, Borrower is currently indebted to Bank pursuant to the terms and conditions of that certain Credit Agreement between Borrower and
Bank dated as of May 1, 2012, as amended from time to time (“Credit Agreement”). 
 WHEREAS, Bank and Borrower have agreed to
certain changes in the terms and conditions set forth in the Credit Agreement and have agreed to amend the Credit Agreement to reflect said changes. 

NOW, THEREFORE, for valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree that the
Credit Agreement shall be amended as follows: 
 1. The following is hereby added to the Credit Agreement as Section 1.1.1.: 

“SECTION 1.1.1. LINE OF CREDIT A. 

(a) Line of Credit A. Subject to the terms and conditions of this Agreement, Bank hereby agrees to make advances to Borrower from time
to time up to and including April 2, 2015, not to exceed at any time the aggregate principal amount of Two Million Four Hundred Thousand Dollars ($2,400,000.00) (“Line of Credit A”), the proceeds of which shall be used to finance
Borrower’s working capital requirements. Borrower’s obligation to repay advances under the Line of Credit A shall be evidenced by a promissory note dated as of May 1, 2013 (“Line of Credit Note A”), all terms of which are
incorporated herein by this reference. 
 (b) Borrowing and Repayment. Borrower may from time to time during the term of the Line of
Credit A borrow, partially or wholly repay its outstanding borrowings, and reborrow, subject to all of the limitations, terms and conditions contained herein or in the Line of Credit Note A; provided however, that the total outstanding borrowings
under the Line of Credit A shall not at any time exceed the maximum principal amount available thereunder, as set forth above.” 

  
 -1- 

 2. Section 1.3. is hereby deleted in its entirety, and the following substituted therefor:

 “SECTION 1.3. COLLATERAL. 

As security for all indebtedness and other obligations of Borrower to Bank under the Line of Credit, Borrower shall grant to
Bank security interests of first priority in all Borrower’s funds deposited in Borrower’s Money Market Account #*. 

As security for all indebtedness and other obligations of Borrower to Bank under the Line of Credit A, Borrower shall grant to
Bank security interests of first priority in all Borrower’s securities account # [*] held with Wells Fargo Institutional Securities, LLC. 

All of the foregoing shall be evidenced by and subject to the terms of such security agreements, financing statements, deeds or mortgages, and
other documents as Bank shall reasonably require, all in form and substance satisfactory to Bank. Borrower shall pay to Bank immediately upon demand the full amount of all charges, costs and expenses (to include fees paid to third parties and all
allocated costs of Bank personnel), expended or incurred by Bank in connection with any of the foregoing security, including without limitation, filing and recording fees and costs of appraisals, audits and title insurance.” 

3. Section 3.1. (b) is hereby deleted in its entirety, and the following substituted thereof: 

“(b) Documentation. Bank shall have received, in form and substance satisfactory to Bank, each of the following, duly
executed: 
 (i) This Agreement and each promissory note or other instrument or document required hereby. 

(ii) Corporate Resolution: Borrowing. 

(iii) Certificate of Incumbency. 

(iv) Security Agreement: Specific Rights to Payment. 

(v) Security Agreement (Financial Assets). 

(vi) Statement of Purpose (Reg. U). 

(vii) Securities Account Control Agreement. 

(viii) Such other documents as Bank may require under any other Section of this Agreement.” 

4. Section 4.3. (a) and (b) are hereby deleted in their entirety, and the following is substituted therefor: 

“(a) not later than each July 15 after and as of the end of each fiscal year, an audited financial statement of
Borrower, prepared by a certified public accountant acceptable to Bank, to include balance sheet, income statement and statement of cash flows; 

(b) not later than 90 days after and as of the end of each fiscal quarter, a financial statement of Borrower, prepared by
Borrower, to include balance sheet and income statement;” 

  
 -2- 

 5. The following is hereby added to the Credit Agreement as Section 6.1. (aa): 

“(aa) The “Margin Value of the Collateral” set forth in the Security Agreement (Financial Assets) executed by
Borrower and delivered to Bank in connection herewith at any time is less than the required amount and Borrower fails to restore such value to the required amount within the period of time specified in said Security Agreement (Financial
Assets).” 
 6. Except as specifically provided herein, all terms and conditions of the Credit Agreement remain in full force and
effect, without waiver or modification. All terms defined in the Credit Agreement shall have the same meaning when used in this Amendment. This Amendment and the Credit Agreement shall be read together, as one document. 

7. Borrower hereby remakes all representations and warranties contained in the Credit Agreement and reaffirms all covenants set forth therein.
Borrower further certifies that as of the date of this Amendment there exists no Event of Default as defined in the Credit Agreement, nor any condition, act or event which with the giving of notice or the passage of time or both would constitute any
such Event of Default. 
 IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be executed as of the day and year first
written above. 
  

									
	PFENEX INC.	 		 	WELLS FARGO BANK, NATIONAL ASSOCIATION
					
	By:	 	 /s/ Bertrand Liang
	 		 	By:	 	 /s/ Linda K. Schneider

		 	Bertrand Liang, Chief Executive Officer	 		 		 	Linda K. Schneider,
		 		 		 		 	Relationship Manager

  
 -3- 

  
 

 
 April 2, 2014 
 Linda
Schneider 
 Senior Relationship Manager 
 Wells Fargo Bank,
National Association 
 San Diego RCB 
 401 B Street, Suite 2201

 San Diego, CA 92101 
  

	RE:	Status of Covenants in regards to revolving line of credit agreement 

 Dear Linda: 

This letter is to confirm the current status of compliance by Pfenex Inc. (“Pfenex”) with the Affirmative and Negative Covenants contained within
the Credit Agreement between Pfenex and Wells Fargo Bank, National Association (“Wells Fargo”), dated May 1, 2012 (the “Agreement”). 

Currently Pfenex is in compliance with all Affirmative and Negative Covenants contained within the Agreement except as specified below: 

 

	 	1)	Pfenex is currently out of compliance in regards to its 2012 audit report (the “2012 Audit Report”), but Pfenex and Wells Fargo agree that if Pfenex provides the 2012 Audit Report and the 2013 audit report to
Wells Fargo on or before May 15, 2014 it will be in compliance with this covenant; 

  

	 	2)	Pfenex has made capital expenditures in the approximate amounts and in the specified periods listed below, which were not pre-approved by Wells Fargo. Wells Fargo is now aware of these capital expenditures and approves
of these capital purchases and Wells Fargo agrees that Pfenex is now in compliance with this covenant 

  

					
	 Period
	  	Amount	  	 
	 May 1, 2012 – December 31, 2012
	  	$310 thousand	  	
	 January 1, 2013 – January 31, 2013
	  	$115 thousand	  	
	 January 1, 2014 – December 31, 2014

budget
	  	$50 thousand	  	

  

	 	3)	Pfenex has entered into a copier lease that was not pre-approved by Wells Fargo. Wells Fargo is now aware of these leases and approves of these leases and Wells Fargo agrees that Pfenex is now in compliance with this
covenant. The relevant information surrounding this copier lease is as follows: 

  

					
	a.	  	Lessor:	  	Canon Financial Services, Inc.
	b.	  	Equipment:	  	Canon IRC Advance 2030 copier
	c.	  	Signed:	  	6.12.2012
	d.	  	First payment due:	  	7.23.2012
	e.	  	Term:	  	60 months
	f.	  	Payment/mo:	  	$140
	g.	  	Total obligation:	  	$8,400
	h.	  	Purchase price:	  	$5,360

 One further point to clarify is that there is an affirmative covenant requiring Wells Fargo’s prior approval
before Pfenex repurchases any of its shares of stock. Pfenex is in the process of repurchasing shares of its stock but this repurchase is required by its Articles of Incorporation. Pfenex’s Articles of Incorporation had been provided to Wells
Fargo prior to entering into the Agreement and therefore Pfenex understood that this acted as an approval of this future repurchase of its stock. However, Pfenex is willing to agree to a threshold wherein if exceeded, Wells Fargo’s prior
approval is obtained. The cumulative threshold for the repurchase of common stock is set at $500,000. 
 If Wells Fargo is in agreement with the compliance
status of the covenants contained within the Agreement please have an authorized representative of Wells Fargo sign in the space provided below. Please feel free to contact me if you have any questions. 

Sincerely, 
 /s/ Bertrand C. Liang 

Bertrand C. Liang, M.D., M.B.A. 
 Chief Executive Officer 

Pfenex Inc. 
 Acknowledged and Agreed: 

Wells Fargo Bank, National Association 
  

	
	/s/ Linda Schneider

 Name: Linda Schneider 
 Title:
Vice President and Relationship Manager 

 WAIVER OF NEGATIVE COVENANT AND EVENT OF DEFAULT 

THIS WAIVER OF NEGATIVE COVENANT AND EVENT OF DEFAULT (the “Waiver”) is given as of May 2, 2014, in favor of Pfenex
Inc., a Delaware corporation (the “Company”), by Wells Fargo Bank, National Association (“Wells Fargo”). Capitalized terms used but not otherwise defined herein shall have the meaning ascribed such terms in the
Credit Agreement. 
 WHEREAS, the Company and Wells Fargo are parties to that certain credit agreement dated as of May 1, 2012, as
amended (the “Credit Agreement”), by and among the Company and Wells Fargo; 
 WHEREAS, pursuant to Section 5.8 of the
Credit Agreement, the Company shall not, without the prior written consent of Wells Fargo, declare or pay any dividend or distribution either in cash, stock or any other property; 

WHEREAS, pursuant to Section 6.1(i) of the Credit Agreement, any change of control of the Company or any entity or combination of
entities that directly or indirectly control the Company may constitute an Event of Default; 
 WHEREAS, the Company is currently
contemplating an initial public offering of its common stock (an “IPO”); 
 WHEREAS, Section (C)4(c) of Article FOURTH of
the Company’s amended and restated certificate of incorporation dated December 1, 2009, as amended, (the “A&R Certificate”) provides that upon the conversion of the Company’s preferred stock to common stock in
connection with an IPO, all accrued but unpaid dividends shall be due and payable (i) in shares of common stock at the fair market value in effect at the time of the conversion, or (ii) in cash, as determined in good faith by the
Company’s board of directors; 
 WHEREAS, in connection with the IPO, the Company intends to issue shares of its common stock to
satisfy all accrued and unpaid dividends upon the conversion of the preferred stock to common stock; 
 WHEREAS, Wells Fargo has agreed to
consent to the issuance of shares of common stock to satisfy the payment of these accrued and unpaid dividends and waive the covenant that Company obtain the prior written consent of Wells Fargo with respect to such dividends; and 

WHEREAS, Wells Fargo has further agreed to waive any Event of Default under Section 6.1(i) arising out of or related to the IPO. 

NOW, THEREFORE, for other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties hereby
agree as follows: 
 1. Waiver of Covenant. Wells Fargo hereby waives the negative covenant set forth in Section 5.8 of the
Credit Agreement with respect to the Company’s obligation to obtain the prior written consent of Wells Fargo for the issuance of the Company’s common stock in connection with the IPO in satisfaction of all accrued and unpaid dividends.

 2. Consent to Payment of Accrued and Unpaid Dividends. Wells Fargo hereby consents to the
issuance of common stock in satisfaction of all accrued but unpaid dividends in connection with the Company’s IPO. 
 3. Waiver of
Event of Default. Wells Fargo hereby waives any Event of Default under Section 6.1(i) of the Credit Agreement arising out of or related to the IPO. 

4. Miscellaneous. Except as set forth herein, the Credit Agreement shall remain in full force and effect. This Waiver may be executed
in counterparts, each of which shall be an original and all of which together shall constitute one and the same instrument. 
 IN WITNESS
WHEREOF, the Parties hereto have duly executed this Waiver to be effective as of the date first above written. 
  

			
	 WELLS FARGO:
  

WELLS FARGO BANK, NA.

		
	By:	 	/s/ Linda Schneider
	Name:  Linda Schneider
	Title:    Vice President
	
	 Agreed and acknowledged:
  

 
 COMPANY:
  

PFENEX INC.
 a Delaware corporation

		
	By:	 	/s/ Bertrand Liang
	Name:  Bertrand Liang
	Title:    Chief Executive Officer

 SECOND AMENDMENT TO CREDIT AGREEMENT 

THIS AMENDMENT TO CREDIT AGREEMENT (this “Amendment”) Is entered into as of June 24, 2014, by and between PFENEX INC., a
Delaware corporation (“Borrower”), and WELLS FARGO BANK, NATIONAL ASSOCIATION (“Bank”). 
 RECITALS 

WHEREAS, Borrower is currently indebted to Bank pursuant to the terms and conditions of that certain Credit Agreement between Borrower and
Bank dated as of May 1, 2012, as amended from time to time (“Credit Agreement”). 
 WHEREAS, Bank and Borrower have agreed to
certain changes in the terms and conditions set forth in the Credit Agreement and have agreed to amend the Credit Agreement to reflect said changes. 

NOW, THEREFORE, for valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree that the
Credit Agreement shall be amended as follows: 
 1. Section 1.3. is hereby deleted in its entirety, and the following substituted
therefor: 
 “SECTION 1.3. COLLATERAL. 

As security for all indebtedness and other obligations of Borrower to Bank under the Line of Credit, Borrower shall grant to Bank security
interest of first priority in all Borrower’s funds deposited in Borrower’s Money Market Account #[*]. 
 As security for all
indebtedness and other obligation of Borrower to Bank under the Line of Credit A, Borrower shall grant to Bank security interest of first priority in all Borrower’s funds deposited in Borrower’s Money Market Account #[*]. 

All of the foregoing shall be evidenced by and subject to the terms of such security agreements, financing statements, deeds or mortgages, and
other documents as Bank shall reasonably require, all in form and substance satisfactory to Bank. Borrower shall pay to Bank immediately upon demand the full amount of all charges, costs and expenses (to include fees paid to third parties and all
allocated costs of Bank personnel), expended or incurred by Bank in connection with any of the foregoing security, including without limitation, filing and recording fees and costs of appraisals, audits and title insurance.” 

2. Section 4.3 is hereby deleted in its entirety, and the following substituted therefor: 

“SECTION 4.3. FINANCIAL STATEMENTS. Provide to Bank all of the following, in form and detail satisfactory to Bank: 

(a) not later than each July 15 and as of the end of each fiscal year, an audited financial statement of Borrower,
prepared by a certified public accountant acceptable to Bank, to include balance sheet, income statement and statement of cash flows; 

  
 -1- 

 (b) not later than July 15, 2014, Borrower’s 2012 fiscal year end
audited financial statement of Borrower, prepared by a certified public accountant acceptable to Bank, to include balance sheet, income statement and statement of cash flows; 

(c) not later than 90 days after and as of the end of each fiscal quarter, a financial statement of Borrower, prepared by
Borrower, to include balance sheet and income statement. 
 (d) from time to time such other information as Bank may
reasonably request.” 
 3. Section 5.2. is hereby deleted in its entirety, and the following substituted therefor: 

“SECTION 5.2. INTENTIONALLY OMITTED.” 

4. Section 5.3 is hereby deleted in its entirety, and the following substituted therefor: 

“SECTION 5.3. LEASE EXPENDITURES. Incur operating lease expense in any fiscal year in excess of an aggregate of $600,000.00.” 

5. Section 5.8. is hereby deleted in its entirety, and the following substituted therefor: 

“SECTION 5.8. INTENTIONALLY OMITTED.” 

6. In consideration of the changes set forth herein and as a condition to the effectiveness hereof, immediately upon signing this Amendment
Borrower shall pay to Bank a non-refundable fee of $250.00. 
 7. Except as specifically provided herein, all terms and conditions of the
Credit Agreement remain in full force and effect, without waiver or modification. All terms defined in the Credit Agreement shall have the same meaning when used in this Amendment. This Amendment and the Credit Agreement shall be read together, as
one document. 
 8. Borrower hereby remakes all representations and warranties contained in the Credit Agreement and reaffirms all covenants
set forth therein. Borrower further certifies that as of the date of this Amendment there exists no Event of Default as defined in the Credit Agreement, nor any condition, act or event which with the giving of notice or the passage of time or both
would constitute any such Event of Default. 

  
 -2- 

 IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be executed as of the day
and year first written above. 
  

									
	PFENEX INC.	  		  	WELLS FARGO BANK, NATIONAL ASSOCIATION
					
	By:	  	 /s/ Bertrand Liang
	  		  	By:	  	 /s/ Linda K. Schneider

		  	Bertrand Liang, Chief Executive Officer	  		  		  	 Linda K. Schneider,
 Relationship
Manager

  
 -3-

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