He will also return 6,665 shares of Diamond stock that were awarded to him after the 2010 financial year. The shares are currently worth about £52,000.
Diamond Foods said the money would be deducted from the £3.4M ($5.4M) that the firm owed to Mendes under the terms of his retirement plan.
Financial irregularities
Mendes has resigned from the firm nine months after being put on administrative leave following an internal investigation revealed financial irregularities. The irregularities forced the firm to restate its finances for 2010 and 2011.
Diamond Foods has also terminated the employment of its former chief financial officer Steven Neil.
Both executives will receive no severance pay, according to the company.
Brian Driscoll, the former head of Hostess Brands, was appointed chief executive in May.
Diamond Foods acquired the Norwich-based Kettle Chips business in 2010.
