Former Bayern Munich coach Louis van Gaal stated in 2010 that Badstuber was the best left footed defender in Germany.

With the arrival of Jupp Heynckes, Badstuber was reinstated at the left of central defense, where he enjoyed a fruitful relationship with fellow international Jérôme Boateng, and helped Bayern maintain 11 clean sheets in a row.

[citation needed] Badstuber injured his anterior cruciate ligament against Borussia Dortmund on 1 December 2012[14] and re–injured it on 19 May 2013, missing the entire 2013–14 season.

[21] He returned to the starting line-up for an 8–0 defeat of Hamburger SV on 14 February 2015 and re-established himself as a first choice player in Pep Guardiola's Bayern team.

[25] It was announced on 23 April 2015 that Badstuber had ruptured his quadriceps muscle in a 6–1 Champions League quarter-final second leg win against Porto and was ruled out for the rest of the season.

[32] Badstuber made his debut for the Königsblauen on 4 February 2017 against his parent club, playing 59 minutes as Bayern were held to a 1–1 draw in Munich.

[33] On 1 March 2017, Badstuber was sent off for two yellow card offences on his second return to the Allianz Arena as Schalke lost 3–0 to Bayern in the quarter-final of the DFB-Pokal.

[35] The following day, 12 May 2017, Bayern Munich released a statement claiming that they had not extended his contract and his time with the club would end at the conclusion of his loan spell.

[36] On 4 August 2017, a few weeks after being released by Bayern Munich, Badstuber announced his return to VfB Stuttgart, the club for whom he played as a young teenager, on a free transfer.

He made his debut in a warm-up match against Hungary on 29 May coming on as a substitute for Arne Friedrich,[43] and was for the first time in the starting lineup in the next game against Bosnia and Herzegovina, the last friendly prior to the World Cup.

After the erratic World Cup, Badstuber improved his performances with consistency and established himself as a starting lineup defender in Löw's team.

In a friendly 3–3 draw on 11 November 2011 against Ukraine, in the international inauguration match of the new Kyiv Olympic Stadion, Löw's experimental formation featured only three defenders, Badstuber was as named the single centre-back.

[45] Badstuber started the first game for Germany in UEFA Euro 2012 helping the team to a clean sheet against Portugal in which the Germans won 1–0.

Due to the fact that Badstuber was injured in December 2012 and only returned to training late during the 2013–14 season, he was not called up for the final 2014 World Cup squad and replaced with youngster Shkodran Mustafi.