On 20 December 2016, Boateng suffered pectoral muscle tendon and was out for almost three months. On 11 March 2017, Boateng made his return after 108 days as a substitute by replacing Javi Martínez in the 64th minute in a 3–0 victory over Eintracht Frankfurt. On 14 April 2017, head coach Carlo Ancelotti confirmed that Boateng was ruled out of the away match in the league against Bayer Leverkusen due to adductor problem. He made his return on 20 May 2017, Boateng sustained muscle injury and was subbed off just after 11 minutes in the last match of the season where Bayern won 4–1 against SC Freiburg. He finished the 2016–17 season with 21 appearances.