From 2002 to 2007, Badstuber progressed through the youth setup at Bayern Munich. He played for Bayern’s reserve team before signing professional terms in July 2009. He had scored four goals in 23 appearances in the Regionalliga Süd during the 2007–08 season and three goals in 32 appearances in the 3. Liga during the 2008–09 season. Badstuber, along with teammate Thomas Müller, having been an unused substitute in a number of first-team matches in the 2008–09 season. He made his debut in the first league game of the 2009–10 season, against 1899 Hoffenheim and has been a regular in defence. He scored his first senior goal, a powerful free kick, against Borussia Mönchengladbach on 4 December 2009. A centre back by trade, he has been playing out of position at left back. The youngster impressed in his first season, and started all league games in the 2009–10 domestic campaign.

On 4 February 2010, Bayern Munich announced that Badstuber had signed a new contract that would keep him at the club until 2014. He finished the 2009–10 season with a goal in 49 appearances.

He was first called up to the senior team as part of the provisional squad for the 2010 World Cup. He made his debut in a warm-up match against Hungary on 29 May coming on as a substitute for Arne Friedrich, 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. Badstuber was then selected in Germany’s 23-man squad for the World Cup finals in South Africa on 1 June, and being handed the squad number 14 shirt by coach Joachim Löw. He started in Germany’s opening group game against Australia at the Durban Stadium, playing the full 90 minutes at left-back and helping the team to a 4–0 victory, it was only his third match in the Germany jersey. Badstuber then started the next group game against Serbia on 18 June 2010 in Port Elizabeth at the Nelson Mandela Bay Stadium. He played 77 minutes, prior to being substituted for fellow Bayern teammate Mario Gómez. He was criticised for his performance and lost his leftback position in the starting lineup to Jérôme Boateng for the rest of the tournament, the 1–0 loss against the Serbs was – so far – the only match in which Badstuber played and Germany lost.

After the erratic World Cup, Badstuber improved his performances with consistency and established himself as a starting lineup defender in Löw’s team. He helped Germany to win all 10 matches of the Mannschaft’s qualification campaign for Euro 2012 to top group A by playing nine out of a possible ten matches, he was only spared in the – for qualification irrelevant – last match against Belgium. During the campaign Badstuber scored his first goal, the 5–1 against Azerbaijan, he headed home a corner kick by Mesut Özil. In a friendly 3–3 draw on 11 November 2011 against Ukraine, in the international inauguration match of the new Kiev Olympic Stadion, Löw’s experimental formation featured only three defenders, Badstuber was as named the single centre back. This was interpreted as a signal that out of many possible candidates, Badstuber had established himself as Löw’s most important player in Germany’s central defense. 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.

Badstuber injured his anterior cruciate ligament against Borussia Dortmund on 1 December 2012 and re–injured it on 19 May 2013, missing the entire 2013–14 season. He had played in 18 matches up until the injury during the 2012–13 season. He returned to first–team training on 5 May 2014 and played in his first match since his injury on 18 July 2014 in a friendly match against FC Memmingen, which Bayern won 3–0. It had been 594 days since the injury.

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.

On 3 February 2013, Badstuber signed a contract extension with Bayern, keeping him at the club until 2017.

Badstuber begun the 2014–15 season as a starting player in Bayern’s first three Bundesliga fixtures. However, a thigh injury sustained against VfB Stuttgart on 13 September kept him out for the rest of the year. 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. On 11 March 2015, Badstuber scored a goal in the 63rd minute in a Champions League match against Shakhtar Donetsk in a 7–0 win. This was his first goal since December 2009 and also his first start in Champions League since 20 November 2012 against Valencia. 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. He finished the 2014–15 season with 16 appearances. He finished the 2015–16 season with nine appearances.

On 19 March 2015, Badstuber was called up to the national team for a friendly match against Australia and a Euro 2016 qualifier against Georgia. He played against Australia on 25 March 2015. This was his first international match since his injury. He had last played in a 4–4 draw against Sweden. Badstuber didn’t fly to Georgia for the European qualifier because of a problem with the hip flexor and later was not included to Euro 2016.

On 10 January 2017, Badstuber joined Schalke 04 on loan until the end of the 2016–17 Bundesliga season. On the same day, it was confirmed by FC Bayern that Badstuber had signed a contract extension with the club lasting until 2018. In the first half of the season, Badstuber had made only one Bundesliga appearance, one DFB-Pokal appearance, and one Champions League appearance for Bayern.

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. 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.

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 finished the 2017–18 season with two goals in 28 appearances.

On 10 July 2018, Badstuber extended his contract with Stuttgart until June 2021.