SAN FRANCISCO — Diamond Foods has agreed to pay $5 million to settle civil fraud charges filed by the U.S. Securities and Exchange Commission over the company’s delayed accounting of payments to walnut growers.

The SEC announced charges on Thursday against Diamond, alleging that the nut and snack maker fraudulently accounted for payments to the growers in order to inflate its earnings for 2010 and 2011. The San Francisco–based company’s former CEO, Michael Mendes, and former CFO, Steven Neil, were also charged for their roles in the scandal.

“Diamond Foods misled investors on Main Street to believe that the company was consistently beating earnings estimates on Wall Street,” Jina Choi, director of the SEC’s San Francisco regional office, said in a statement. “Corporate officers cannot manipulate fiscal numbers to create a false impression of consistent earnings growth.”

Mendes will pay $125,000 to settle the negligence claims filed against him. The SEC claims that Mendes, who certified Diamond’s financial statements, should have known the company was reporting inaccurate walnut costs.

“Mr. Mendes is pleased to put this matter behind him and move forward in his professional life,” said his lawyer, Sidley Austin partner Sara Brody.

Neil, who is accused of directing the scheme, is fighting the charges filed against him. Facing pressure to boost Diamond’s earnings as the price of walnuts skyrocketed, Neil schemed to understate the company’s payments to walnut growers, the SEC alleges.

Neil’s lawyer, Hogan Lovells partner Michael Shepard, said his client looks forward to rebutting those claims at trial.

“Steven Neil did nothing wrong,” Shepard said. “He followed longstanding company processes, and he followed an accounting treatment approved by the company’s outside auditors.”

Both Mendes and the company agreed to settle the charges without admitting wrongdoing.

Diamond general counsel Stephen Kim and outside counsel Susan Muck did not respond to requests for comment. Represented by Fenwick & West, Diamond struck a deal in August to settle a securities class action over the accounting scandal for $96 million. Comprised of $11 million in cash and more than 4 million shares of stock, the settlement was crafted to keep Diamond intact, lawyers for lead plaintiff Mississippi Public Employees Retirement System wrote in court papers.

Contact the reporter at jlove@alm.com.