He criticised the "frustrating process" of trying to negotiate with the corporation and said he wondered if the BBC understood "the realities of today's commercial world".
It is understood that Roux, who has fronted MasterChef: The Professionals for six years and revived the series Food And Drink last year, had been unable to come to a deal about the level of his commercial activity.
Among his advertising commitments has been a deal with potato firm Albert Bartlett, for which he was an ambassador.
Roux, 53, whose restaurant Le Gavroche has two Michelin stars, said: "This hasn't been an easy decision for me to make. I love working with the BBC, and am very proud of how we have built up the popularity and success of these two iconic shows.
"It's not for lack of trying, but sometimes negotiating with the BBC can be a frustrating process, and there are times when I have wondered if the corporation understands the realities of today's commercial world.
"The BBC needs to recognise the value of the talent they work with, and also that, whilst we love to be associated with top-quality television, we have other professional commitments that are as important to us as programme-making."
The BBC issued a statement confirming the chef's decision to leave "due to a conflict in his commercial interests" and thanking him for the "huge contribution" he had made to the shows