Exhibit 10.17

THIRD AMENDMENT TO CREDIT AGREEMENT

THIS AMENDMENT TO CREDIT AGREEMENT (this “Amendment”) is entered into as of the
last date of execution by both parties (the “Effective Date”), 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 2.6 is hereby deleted in its entirety, and the following substituted
therefor:

“SECTION 2.6. INCOME TAX RETURNS. Except as disclosed to Bank in writing no
later than November 21, 2014, Borrower has no knowledge of any pending
assessments or adjustments of its income tax payable with respect to any year.”

2. 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 $850,000.00.”

 

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3. 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.

4. 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 BETRAND LIANG, LINDA K.
SCHNEIDER, CHIEF EXECUTIVE OFFICER RELATIONSHIP MANAGER Date: 12/11/14 Date:
12/11/2014

 

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