In April 2013, a €37 million bid from Bayern Munich triggered a release clause in Götze's contract, making him the second-most expensive German player at the time, behind Mesut Özil.

[8] He made his Bundesliga debut on 21 November 2009 in a scoreless draw against Mainz 05, coming on as a substitute for Jakub Błaszczykowski in the 88th minute.

[20] At Barcelona Lionel Messi, Andrés Iniesta and Xavi are building a triangle, but as a classic duo there is nobody better than the prolific Reus and Götze.

[32] Dortmund coach Jürgen Klopp claimed that the reason behind Götze's transfer to Bayern was the playmaker's wish to play under manager Pep Guardiola, formerly of Barcelona.

[33] Klopp admitted his annoyance at the timing of the announcement of Götze's move, as it was barely 36 hours before Dortmund's Champions League semi-final with Real Madrid.

[37] On 23 October, Götze scored his first competitive goal for Bayern in a 5–0 Champions League group stage win over Viktoria Plzeň at the Allianz Arena.

[38] On 26 October 2013, Götze came on as a substitute for Toni Kroos in the 25th minute and scored his first Bundesliga goal for Bayern Munich with a header in a 3–2 win against Hertha BSC.

[41] In the team's next fixture against CSKA Moscow, Götze scored the second goal of 3–1 away win in the 2013–14 UEFA Champions League group stage.

[42] On 7 December, Götze helped Bayern by netting a goal in the closing minute, as well as assisting Thomas Müller, in a dominant 7–0 away victory over Werder Bremen.

[43] On 17 December, Götze scored a long-range goal in the 47th minute against the AFC champion Guangzhou Evergrande, helping Bayern win 3–0 and advance to 2013 FIFA Club World Cup Final,[44][45] where he came on as an 80th-minute substitute.

[45][51][46][52] After helping Germany win the 2014 FIFA World Cup, Götze began the 2014–15 season on 14 August 2014, coming on as substitute in a 2–0 loss against Borussia Dortmund in 2014 DFL-Supercup.

[61] On 28 April 2015, Götze was one of four Bayern players to miss in a 2–0 penalty shootout defeat to Borussia Dortmund in the DFB-Pokal semi-final.

On 16 September, Götze, coming on as a substitute in 79th minute, scored the second goal against Olympiacos in the 2015–16 Champions League as his club earned a 3–0 away win.

[79] After a long time of re-adapting to the Dortmund system, Götze managed to find his form when their side faced Bayern Munich on 20 November 2016.

[81] In February 2017, Götze was dropped from the Dortmund team with a mystery illness, identified in media reports as myopathy, a metabolic disease which can cause fatigue and weight gain.

[84] After his absence due to metabolic illness, Götze returned to the field on 14 July 2017 where Dortmund successfully defeated Urawa Reds 3–2 in a friendly match.

[86] After the match, Dortmund's coach Peter Bosz hailed Götze's performance, but stated that he needs to be careful with his midfielder in order to gain full recovery.

[89] On the opening day of the 2019–20 Bundesliga campaign, Götze made his 200th competitive appearance for Dortmund, coming on as a second-half substitute for Reus in a 5–1 win over Augsburg.

[90] On 23 May 2020, Borussia Dortmund sporting director Michael Zorc stated that Götze would leave the club at the end of the season.

He made his debut that day, coming on in the 78th minute in a goalless draw, substituting for his Dortmund teammate Kevin Großkreutz[101] and becoming the youngest German international since Uwe Seeler.

[105] Götze contributed four goals in 2014 FIFA World Cup qualifying, and was named in Germany's squad for the tournament finals.

"[113] Götze scored the only goal of the match in the 113th minute, controlling André Schürrle's cross on his chest before volleying the ball into the net, giving Germany their fourth World Cup.

[119] In the lead up to the 2018 FIFA World Cup, he played in a friendly against France in November 2017 after a one-year absence from the national team, but ultimately did not make the squad for the final tournament.

[123] Götze was considered to be one of the best young players in the world, possessing speed, technique, dribbling skills and playmaking capabilities.

Following the departure of fellow playmaker Shinji Kagawa in 2012, during the 2012–13 season, Klopp assigned Götze as central attacking midfielder.

[125] However, Götze's pace deteriorated before the peak age of an average professional footballer, and this was seen as one of the reasons for his second departure from Borussia Dortmund.

[142] The health condition was later found out to be myopathy, a muscular disorder which affects the fibres in the muscles, meaning they do not function correctly.

Speaking about discovering the health condition Götze released a statement via the Borussia Dortmund official website which read, "I'm currently undergoing treatment and will do everything in my power to be back in training and helping my team to achieve our common goals as soon as possible".

[144] He appeared in an advert for the Nike Green Speed II alongside Eden Hazard, Theo Walcott, Raheem Sterling, Christian Eriksen and Stephan El Shaarawy in November 2012.

[146] Götze appeared as part of a Galaxy XI in an advertisement for South Korean company Samsung alongside Cristiano Ronaldo, Lionel Messi, Wayne Rooney, Radamel Falcao and Iker Casillas in a team managed by German football legend Franz Beckenbauer.