His decision to stand down from the non-executive role follows a 37% plunge in profits at Warburtons, to £16.3m in 2011.
The company attributed the plunge, which was disclosed in June, to a restructure at its bakery operations.
In the 12 month period to 24 September 2011, Warburtons reported turnover of £495m, compared to £492m the year before. Profits slumped 37% to £16.3m.
Today AG Barr, the drinks brand, said Warburton was stepping down "to focus more on his role at Warburtons."
The fifth-generation Warburton has held the position of chairman at the family run business since 2001. He assumed control of the company in 1991, alongside cousins Brett and Ross.
AG Barr has appointed John Nicholson, a senior executive at Heineken, to the role of non-executive director.
Nicholson is currently president of Heineken Americas, based in New York. He will join the board in January.Follow @johnreynolds10