For 2021, Bagnaia moved up to the factory Ducati Lenovo team along with former teammate at Pramac Jack Miller. He qualified for pole position ahead of teammate Miller and the factory Yamaha riders Fabio Quartararo and Maverick Vinales at Losail. This marked his first MotoGP pole position. He would later finish 3rd. Bagnaia qualified 6th in the 2021 Doha motorcycle Grand Prix. During the race, he was able to push up to 3rd place, but a mistake caused him to run wide and dropped to 6th place. At Portimao Bagnaia initially took Pole position during Qualifying, however his lap time was disallowed due to Miguel Oliveira's crash and yellow flag, which meant Bagnaia started the race from 11th grid position. During the race Bagnaia worked his way up to finish in 2nd place behind Fabio Quartararo after riders Jack Miller, Alex Rins and Johann Zarco all crashed out.