UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 8-K/A

(Amendment No. 1)

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of the Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): June 14, 2013

VERENIUM CORPORATION

(Exact name of registrant as specified in its charter)

Registrant’s telephone number, including area code: (858) 431-8500

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

EXPLANATORY NOTE

This Amendment No. 1 to the Current Report on Form 8-K (this “Amendment”) amends the Current Report on Form 8-K filed by Verenium Corporation (the “Company”) with the Securities and Exchange Commission on June 19, 2013 (the “Original Form 8-K”). The Original Form 8-K reported the final voting results of the Company’s 2013 Annual Meeting of Stockholders held on June 14, 2013 (the “Annual Meeting”). The sole purpose of this Amendment is to disclose the Company’s decision regarding how frequently it will conduct future stockholder advisory votes to approve compensation of the Company’s named executive officers (“say on pay votes”). No other changes have been made to the Original Form 8-K.

Item 5.07 Submission of Matters to a Vote of Security Holders.

As previously reported in the Original Form 8-K, in a non-binding advisory vote on the frequency of future say on pay votes held at the Annual Meeting, 2,625,596 shares were voted in favor of holding say on pay votes every year, 19,043 shares were voted in favor of holding say on pay votes every two years and 667,072 shares were voted in favor of holding say on pay votes every three years. The Company considered the outcome of this advisory vote at a meeting of its board of directors on August 1, 2013 and determined, as was recommended with respect to this proposal by the Company’s board of directors in the proxy statement for the Annual Meeting, that the Company will hold future say on pay votes every one year until the occurrence of the next advisory vote on the frequency of say on pay votes. The Company is required to hold the next advisory vote on the frequency of say on pay votes no later than the annual or other meeting of stockholders of the Company held in the sixth calendar year after the vote held at the Annual Meeting.

SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.