Wilson, who has previously held roles at Kraft, Allied Lyons, Reckitt Benckiser and Vileda, joined Allied in 2005 as head of marketing for Kingsmill before moving to the director role the following year.
Allied Bakeries did not state when he will exit the business.
His departure comes a month after the bakery company announced plans to cut 23 management and admin positions at its HQ in Maidenhead and its Liverpool site, including the role of category director.
Earlier this year the company was joined by Jon Jenkins, the former boss of Twinings Tea, as managing director.
Commenting on the departure of Wilson, Allied said: “We can confirm that following 10 years with Allied Bakeries, Jon Wilson will be leaving the business. Allied Bakeries is thankful for Jon’s hard work at the head of the marketing function. Under his leadership, the Kingsmill portfolio has grown significantly to introduce a number of new innovations to the market.”
Two weeks ago, in a pre-close update for the year to 12 September, Associated British Foods, the parent company of Allied Bakeries, said the UK bread market remained “challenging” and that lower bread prices had resulted in lower profitability - despite the Kingsmill brand being relaunched in May and revenues from Sandwich Thins continuing to build following last year’s launch.