Müller started the season by winning and scoring in the 2016 German Super Cup against Borussia Dortmund on 14 August 2016. In the league, Müller did not score for 999 minutes until he scored during a home game against VfL Wolfsburg in the 76th minute. He finished the 2016–17 season by scoring five goals in 29 Bundesliga appearances, no goals in three German Cup appearances, and three goals in nine Champions League appearances. Müller did have a career best 12 assists in the Bundesliga.