The retailer has closed the dedicated depot at Sherburn-at-Elmet and awarded a new distribution contract to TDG.
The logistics company, which works with Tesco and Sainsbury, has taken over supply of all ambient and frozen products to Kwik Save's 184 UK stores in an deal worth £9m a year.
Store deliveries will be made from TDG's distribution centre at Appleton Link, near Warrington. "We are working with new suppliers and have chosen to work with a third party with retail food expertise," said David Birchall, Kwik Save commercial director.
Sources told The Grocer about poor on-shelf stocks levels, with 75% availability in one store. Another said that tobacco fixtures in two stores in the Birmingham area were virtually bare.
However, a spokeswoman for Kwik Save said: "We have been agreeing tobacco supply lines and all stores are now being fully replenished. Contracts are in place for other categories."
Suppliers will be required to deliver frozen food to TDG's warehouse in Manchester for storage before it is transferred to the Warrington depot.
News of the overhaul was overshadowed by the departure of Kwik Save MD Paul Niklas and finance director Steve Payne.