During the 2012–13 season, Boateng was a regular member of the Bayern team that won a treble of the Bundesliga, DFB-Pokal and Champions League, in addition to the DFL-Supercup at the start of the season. On 5 December 2012, Boateng picked up a red card against BATE Borisov which resulted in a two-match ban. He scored his first Bundesliga goal with a header from Phillip Lahm's cross on 9 March 2013, the winner as Bayern came from behind for a 3–2 home win against Fortuna Düsseldorf. He netted a second on 13 April, an acrobatic half-volley to open a 5–0 home win over 1. FC Nürnberg, after Bayern had already won the league title. He scored two goals in 40 appearances during the 2012–13 season.