FC Bayern Munich made few squad changes for the 2008–09 season. With captain Oliver Kahn retiring and coach Ottmar Hitzfeld leaving to coach the Swiss national team, the team leaders had to be replaced. Jürgen Klinsmann was appointed as new coach as announced in December 2007. In August 2008, Klinsmann announced that Mark van Bommel would succeed Kahn as captain. Klinsmann was sacked in April 2009 when the club officials saw the club's minimum aim, qualification for the Champions League, in jeopardy after a string of games in which Bayern underperformed. Jupp Heynckes was appointed as caretaker manager.

With Ottmar Hitzfeld not available for another season, Bayern announced in December 2007 that they had signed former Bayern player and recent manager of the German national team Jürgen Klinsmann as head coach for the 2008–09 season. Oliver Kahn had, even before the 2007–08 season, announced that this would be his last season as a player. He was replaced by former reserve goalkeeper Michael Rensing, whose spot was taken by the newly signed Hans-Jörg Butt. Second reserve goalkeeper Bernd Dreher had also retired and was replaced by the amateur Thomas Kraft. Reserve strikers Jan Schlaudraff (to Hannover 96) and Sandro Wagner (to MSV Duisburg) left the club, but found no replacements. After being loaned out for two seasons, midfielder Julio dos Santos left the club for good. The only field player added to the squad was Tim Borowski, who came from Werder Bremen. All changes were made before UEFA Euro 2008. After the tournament, Bayern announced that they would make no further squad changes.

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