For 2021, Morbidelli's team mate is the VR46 Academy owner Valentino Rossi. In this season, Morbidelli still rides with his 2019 "A-spec" Yamaha. Morbidelli took his first podium at Jerez, finishing third behind Jack Miller and Francesco Bagnaia. After the German Grand Prix, Morbidelli injured his knee in a training accident and was unable to race at Assen when he was substituted by Yamaha World Superbike rider Garrett Gerloff, and the Styrian event in Austria by Yamaha factory tester Cal Crutchlow.