Exhibit 99.1

FOR IMMEDIATE RELEASE

VERENIUM REPORTS FINANCIAL RESULTS

FOR THE SECOND QUARTER AND SIX MONTHS ENDED JUNE 30, 2013

SAN DIEGO, Calif., August 7, 2013 – Verenium Corporation (Nasdaq: VRNM), a leading industrial biotechnology company focused on the development and commercialization of high-performance enzymes, today reported operating highlights and financial results for the second quarter and six months ended June 30, 2013.

Operating Highlights

Since the beginning of 2013, the Company has made important progress on both operational and financial fronts. Recent accomplishments include:

Animal Health and Nutrition

Grain Processing

Oilfield Services

Expansion Pipeline

Financial Results

Revenues

Revenues for the periods ended June 30, 2013 and 2012 were as follows (in thousands):

Total revenues for the six months ended June 30, 2013 decreased 11% to $29.2 million from $32.9 million in the prior year, due in large part to license revenue recorded in 2012 from DSM and Novus. Combined product and contract manufacturing revenue for the six months ended June 30, 2013 decreased 2% to $26.0 million from $26.4 million in the prior year.

Product revenue for the six months ended June 30, 2013 decreased 11% to $21.2 million from $24.0 million in the prior year, primarily attributed to a decline in Phyzyme^® XP phytase manufacturing revenue due to an increase in manufacturing volumes by DuPont, the Company’s marketing and distribution partner for Phyzyme^® XP phytase. Revenue associated with product manufactured at DuPont sites is recognized on a net basis equal to the royalty on operating profits received from DuPont, and excludes gross manufacturing revenue.

In addition, grain processing revenue declined during the first quarter of 2013 and was offset in part by an increase in grain processing revenue during the second quarter of 2013, indicative of improvements in corn ethanol market conditions and increased customer adoption of the Company’s Fuelzyme^® alpha-amylase enzyme.

The Company also reported lower revenue from its grain processing and oilseed processing product lines as a result of the sale of its Veretase^® alpha-amylase and Purifine^® PLC enzymes to DSM in March 2012. In conjunction with the sale to DSM, the Company entered into a supply agreement to continue to produce and sell Purifine^® PLC and Veretase^® alpha-amylase products to DSM at lower sales prices than prior periods when sold directly to end customers. Revenue from the DSM supply agreement is reported as contract manufacturing revenue.

Gross Profit and Gross Margin

Product and contract manufacturing gross profit for the six months ended June 30, 2013 increased to $9.6 million from $9.2 million for the same period in 2012. Gross margin increased to 37% for the six months ended June 30, 2013, as compared to 35% for the same period in 2012, attributed primarily to improved manufacturing yields.

Operating Expenses

Excluding cost of product and contract manufacturing revenues, total operating expenses for the six months ended June 30, 2013 increased to $20.3 million from $17.2 in the prior year. This increase is primarily due to increased research and development costs reflecting continued investment in pipeline products, including the launch of two new products during the first half of 2013, and the expected launch of one more product by the end of the year.

Income (Loss) from Operations

Loss from operations for the six months ended June 30, 2013 was $7.5 million compared to income from operations of $29.7 million for the prior year, on a GAAP accounting basis, including the impact of the $31.3 million gain on sale of the oilseed processing business to DSM in 2012.

Adjusted EBITDA

As detailed in the attached financial tables, the operating results for the first half of the current and prior year were impacted by significant non-recurring and non-cash items. The Company believes that reporting Adjusted EBITDA on a non-GAAP basis, which excludes the impact of these items, provides a more consistent measure of operating results. It should not be considered, however, in isolation or as a substitute for, or superior to, the financial information presented in the Company’s consolidated financial statements. Further, the Adjusted EBITDA measure shown for the Company may not be comparable to similarly titled measures used by other companies.

The Company reported Adjusted EBITDA loss of $5.1 million for the six months ended June 30, 2013 compared to $0.5 million for the same period in 2012. The change in Adjusted EBITDA is primarily attributed to license revenue recorded in 2012 from DSM and Novus International, and increased research and development expenses.

Balance Sheet

The Company ended the quarter with $21.7 million in cash and cash equivalents and $2.5 million in total restricted cash.

“In 2013, we’ve gained substantial traction with prospective customers for our grain processing products and expanded our presence in our core markets with the introduction of three new products,” said James Levine, President & Chief Executive Officer at Verenium. “Looking

forward we are excited to launch our new phytase enzyme product, CIBENZA^® PHYTAVERSE™, with partner Novus later this year.”

About Verenium

Verenium, an industrial biotechnology company, is a global leader in developing high-performance enzymes. Verenium’s tailored enzymes are environmentally friendly, making products and processes greener and more cost-effective for industries, including the global food and fuel markets. Read more at www.verenium.com.

Forward-Looking Statements

Statements in this press release that are not strictly historical are “forward-looking” and involve a high degree of risk and uncertainty. These include, but are not limited to, statements related to Verenium’s technology, products and product candidates (including, in each case, their value, potential for revenue growth and expected near-term and longer term revenue)and product pipeline (including the timing for commercial launch of any product candidates), lines of business, operations (including Verenium’s ability to successfully negotiate and enter into future collaborations and partnerships), capabilities, commercialization activities, customer adoption rates, industry conditions, future financial performance (including all financial guidance), and near-term and longer-term growth and prospects. Such statements are only predictions, and actual events or results may differ materially from those projected in such forward-looking statements. Factors that could cause or contribute to the differences include, but are not limited to, risks associated with Verenium’s strategic focus, technologies, products and product candidates and product pipeline (including Verenium’s ability to identify, develop and commercialize new products and product candidates, either independently or with collaborators or partners, and market demand for those products and product candidates), dependence on patents and proprietary rights, protection and enforcement of its patents and proprietary rights, the commercial prospects of the industries in which Verenium operates and sells products, Verenium’s dependence on manufacturing and/or license agreements, its ability to achieve milestones under existing and future collaboration agreements, the ability of Verenium and its partners to commercialize its technologies and products (including by obtaining any required regulatory approvals) using Verenium’s technologies, the timing for launching any commercial products and projects, the ability of Verenium and its collaborators to market and sell any products that it or they commercialize, the development or availability of competitive products or technologies, the future ability of Verenium to enter into and/or maintain collaboration and joint venture or partnership agreements and licenses on a timely basis or at all, and risks and other uncertainties more fully described in Verenium’s filings with the Securities and Exchange Commission, including, but not limited to, Verenium’s annual report on Form 10-K for the year ended December 31, 2012 and any updates contained in its subsequently filed quarterly reports on Form 10-Q. These forward-looking statements speak only as of the date hereof, and Verenium expressly disclaims any intent or obligation to update these forward-looking statements.

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Contacts:

Verenium Corporation

Condensed Consolidated Statements of Operations

(unaudited, in thousands, except per share amounts)

Verenium Corporation

Condensed Consolidated Balance Sheet Data

(unaudited, in thousands)

Verenium Corporation

Unaudited Supplemental and Non-GAAP Financial Information

(in thousands)

The following Adjusted EBITDA figures represent supplemental and non-GAAP financial information, and is derived from the Company’s condensed consolidated financial statements for the three and six months ended June 30, 2013 and 2012, as reported under GAAP. The Company believes that such supplemental and non-GAAP financial information is helpful to understand the results of operations of the business. It should not be considered, however, in isolation or as a substitute for, or superior to, the financial information presented in the Company’s consolidated financial statements. Further, the Adjusted EBITDA measure shown for the Company may not be comparable to similarly titled measures used by other companies.