On 10 May 2016, it was confirmed that Hummels would re-join Bayern Munich from 1 July 2016, signing a five-year contract. He made his 2016 debut for Bayern on 14 August 2016 in the German Super Cup final, against his old team and winning 2–0. On 20 August, Hummels scored his first goal for the club in a 5–0 victory over Carl Zeiss Jena during the DFB-Pokal match. On 26 November, Hummels scored his first league goal for the club in a 2–1 win over Bayer Leverkusen. On 24 September, Hummels suffered knee injury in his right knee just before half time and was subbed off in a 1–0 victory over Hamburger SV. He made his comeback as a substitute in the second half in a 1–0 defeat to Atlético Madrid on 29 September. On 11 March 2017, Hummels made a world class goal-saving tackle on Eintracht Frankfurt's Branimir Hrgota by making an amazing run towards him and denied him to score from a clear chance. On 9 April, Hummels missed the Champions League quarter-final first leg against Real Madrid after sustaining an ankle injury in training. On 19 April, he did not fully recover from the injury and had to play the second leg against Real Madrid as defender Javi Martínez was shown red card in the first leg and there was no more backup player in centre-back position, but the match ended 4–2 defeat for his side as they got knocked out from the competition. On 26 April, Hummels scored a goal against his former club Borussia Dortmund in a 2–3 loss in the DFB-Pokal semi-final. He finished the 2016–17 season with three goals and two assists in his forty-one matches. Hummels finished the 2016–17 season with three goals in 42 matches played.