The celebrity chef - who appeared on the show's panel from the very first series in 2008 - was forced to exit the show because of a business conflict.
"MasterChef is sad to announce after a very happy relationship with Michel Roux Jr as one of the judges on the Professionals series that he will no longer be appearing on the BBC due to a conflict in commercial interests," the show announced on its Facebook page.
"Chef Michel has been a committed and extremely well loved and respected member of the MasterChef team, an inspiration for the young chefs who have appeared on the show and those he works with on behalf of MasterChef off camera.
"We wish him the very best of luck in everything he does."
News on who will replace Roux Jr on the judging panel has not yet emerged, though the show vowed that a new series will "still go ahead in the autumn".
Casting for the new episodes is currently taking place on the show's official website.