Baker began 2012 on the disabled list due to elbow tendinitis. He made a rehab start with the Class A Fort Myers Miracle in their first game of the season but threw just 11 pitches in the start before leaving the game after talking to the trainers. It was announced on April 11 that Baker would miss the entire 2012 season with Tommy John surgery. Baker said, "It's something that I've been battling for a while. I don't mind pitching through pain, as long as you don't have the chance to further the injury. But when it comes to a point where your velocity's not there and you don't have the ability to finish pitches like you know you're capable of doing, then something's got to be done." On October 29, the Twins announced they declined their club option for Baker worth $9.25 million, ending Baker's tenure with the team.