The company also fired its former chief financial officer, Steven Neil, it said in a regulatory filing on Wednesday.

The maker of Emerald nuts, Kettle chips and Pop Secret popcorn recently restated financial results for fiscal years 2010 and 2011 after an internal probe found that it had accounted for some payments to farmers in the wrong fiscal periods.

The scandal led to the ouster of Mendes and Neil in February and the appointment of former Hostess Brands chief Brian Driscoll as chief executive in May.

Under a separation agreement, Mendes will repay the company $2.7 million, which was his total bonus for fiscal 2010 and fiscal 2011, and return 6,665 shares of Diamond stock that were awarded to him after fiscal 2010.

The cash amount will be deducted from the $5.4 million that Diamond owes to Mendes under his retirement plan, the company said in the filing.

Both executives will not receive any severance payment, the company said.

Diamond Foods shares, which have fallen 59 percent this year, closed at $13.09 on the Nasdaq on Tuesday.

(Reporting by Siddharth Cavale; Editing by Anthony Kurian and Saumyadeb Chakrabarty)