Kwik Save has lost its second chief executive since it was bought from Somerfield by a private equity firm in February.
Andrew Villars, who had headed up Kwik Save since July, has stepped down.
The retailer is understood to have raised £30 million from private investors in order to purchase 455 ex-Somerfield outlets and revamp its existing 180 stores.
Kwik Save said there would be no redundancies as a result of the acquisition.