The following year, Petrucci joined the Ioda Racing Project team in MotoGP and saved his best result for last, finishing 8th in Valencia. He ended his rookie year in 19th place with 27 points. Staying with the same team in 2013, Petrucci ended the season in 17th place with an 11th place in Catalonia as his best result. In 2014, a left-wrist fracture sustained after a crash in the Spanish GP warm-up forced Petrucci to miss four races. Danilo finished the season in 20th place with 17 points and an 11th place in Aragon as his best result.
In 2015, Petrucci became part of the Ducati family joining the Pramac Racing Team, and he immediately showed good chemistry with the Desmosedici GP bike. After claiming an impressive 2nd place in the British GP at Silverstone, he finished the season in 10th position (113 points). The following year, Petrucci once again rode the Ducati Desmosedici GP of the Pramac Racing Team but suffered an unfortunate start to his season, when he seriously injured a right hand during the Australian tests and had to miss the first four races. After starting his championship quest at Le Mans, he finished the year in 14th position with a 7th place in Czech Republic as his best result.