During his first year in Bayern's academy, Can was used in the centre-back position before returning to midfield when he began playing for Bayern Munich II in the Regionalliga Bayern. He made his first team debut in the 2012 DFL-Supercup and his Bundesliga debut against 1. FC Nürnberg on 13 April 2013. His first and only league goal for the club came on 27 April 2013 in a 1–0 home win over SC Freiburg. Competing with Bastian Schweinsteiger, Luiz Gustavo and Javi Martínez for a spot in Bayern's midfield, he ultimately made only seven senior appearances before signing for fellow Bundesliga side Bayer Leverkusen in 2013 in seek of regular game-time.