Thomas, currently senior buying manager for potatoes, is going into corporate purchasing, where he will take up the role of senior buying manager for global transportation.
"Paul has made a significant contribution to the area during what has been a difficult season," Tesco said in a statement.
Thomas's replacement, Andrew Blackett, joined the fresh foods department on Monday, having been promoted to senior buyer. He was previously buying manager for counters and has worked at Tesco for 21 years. He would "bring a wealth of operational and commercial experience", Tesco said.
There has been a string of high-profile departures from Tesco's fresh foods section over the past few months. Earlier this year, fresh food category director Alex Dower moved to Pret A Manger and category director Tim Lee joined Tesco's US Fresh & Easy venture. In June, commercial director for fresh foods Colin Holmes quit in the wake of the announcement by CEO Sir Terry Leahy that he planned to retire.