Throughout the 2010–11 season he made 32 appearances in all competitions for Bayern. During the 2010–11 season, Badstuber endured a tumultuous relationship with coach Louis van Gaal, who despite stating that he has high trust in Badstuber, strongly criticized him following a number of poor performances. As a result of his poor form he found himself out of the starting eleven several times throughout the season. 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. Additionally, he was integral to the Bayern Munich defensive line which lead the team to the 2012 UEFA Champions League Final, beating Real Madrid, Napoli and Manchester City along the way, before losing out to English side Chelsea in the final. He made 50 appearances across all competitions during the 2011–12 season.