Bayern were the reigning Bundesliga and DFB-Pokal champions, and therefore also participated in the German super cup, the DFL-Supercup.

[7] In August, Carlo Aneclotti named his son Davide as assistant coach, joining Clement and Gerland.

[11][12] Patrick Weihrauch, who never made a senior appearance for Bayern, also left the club for Würzburger Kickers on 2 June.

[13] On 6 June, after making 17 appearances in all competitions during the 2015–16 season, Sebastian Rode left the club for Borussia Dortmund.

[18] The new season officially began on 11 July 2016 with the presentation of Carlo Ancelotti as new manager and a training session.

[19] Jérôme Boateng, Manuel Neuer, Joshua Kimmich, Thomas Müller, Mats Hummels, Robert Lewandowski, Kingsley Coman, and Renato Sanches were all given an extended break until 5 August after UEFA Euro 2016.

[28] As Bayern completed the domestic double the previous season, Dortmund qualified as league runners-up.

Bayern won the match 2–0 with second half goals from Arturo Vidal and Thomas Müller, after being outplayed in the opening 45 minutes.

[31] Bayern qualified automatically for the UEFA Champions League group stage after winning the Bundesliga the previous season.

Bayern were placed in Pot 1, and were drawn into Group D, along with Atlético Madrid, who knocked them out of the semi-finals in the previous season, PSV Eindhoven, and Rostov.

[33] Bayern Munich were selected to face Werder Bremen at home in the season opener on 26 August.

[33] Bayern won the match 6–0, making it the biggest win by a defending champion to start the season.

[36] On 13 September, Bayern faced Russian side Rostov at home for the first Champions League fixture.

Bayern won the match 5–0, with Lewandowski converting a penalty in the 28th minute before Müller scored on his birthday during second half stoppage time.

[38] On 21 September, matchday 4 of the Bundesliga, Bayern played at home against Hertha BSC, who were second in the table and had a perfect record.

The match was scoreless until the 88th minute, when Kimmich scored the lone goal, giving Bayern the late victory.

[40] On 28 September, Bayern faced Spanish side Atlético Madrid away on matchday 2 in the Champions League.

Although having numerous opportunities, Bayern were unable to equalise, and in the 84th minute, Atlético were given a penalty after a poor challenge by Vidal on Filipe Luís.

Bayern had numerous opportunities, but were unable to capitalise, making it two winless games in a row for the Bavarians.

The DFB Sports Court handed Starke a one match suspension, making him unavailable for selection against Borussia Mönchengladbach.

[44] On 19 October, Bayern met Dutch side PSV Eindhoven at home on matchday 3 of the Champions League.

Only two minutes in the second half, Augsburg were awarded a penalty after Hummels knocked Gojko Kačar to the ground.

[47] Following the match, Bayern were drawn against VfL Wolfsburg in the round of 16 of the DFB-Pokal, to take place on 7–8 February 2017 at home.

Santiago Arias opened the scoring for PSV with a possibly offside header past Neuer.

The score remained level until the 73rd minute, when Lewandowski completed a brace with a goal following a cross from Alaba.

The match finished as a 1–1 draw, keeping Bayern at the top of the table based on goal difference.

Bayern equalised in the 34th minute via an own goal from Steven Zuber after a cross from Douglas Costa intended for Lewandowski.

[51] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.