Stewart Ross set up the award-winning brewery with Chris Ives in 2008. He left the company on November 30.
In a statement, Ilkley Brewery said Mr Ross “has worked alongside its other directors to achieve his goal of re-establishing brewing in Ilkley following the closure of the original Ilkley Brewery and Aerated Water Company in 1920.
“As Stewart moves on to new challenges, Ilkley Brewery wishes him the best for the future and Stewart wishes the brewery continued success.”
Mr Ross, who declined to comment on his departure, told the Yorkshire Post how he and a group of local investors plan to refurbish the Albert pub on Skipton Road and install a brewing plant at the back of the building.
The pub will be renamed the Flying Duck in a nod to its past as the Mallard and it will be home to the new Wharfedale Brewery.
Mr Ross said the investors are spending around £160,000 on the venture. One of them bought the pub four years ago.
Meanwhile, Ilkley Brewery directors Chris Ives and Richard Shelton last night launched their first new brew of the year, The Mayan, at the historic Whitelock’s pub in central Leeds.
Mr Ives said the brewery plans to increase production by 15-20 per cent and is set to complete its first export this year, to the US.