The 2009–10 season of Bayern Munich began on 1 July with their first training session, led by the team's new head coach Louis van Gaal. After several friendlies the first competitive game was a cup game on 1 August. The league started on 8 August.

Bayern made several squad changes, signing Alexander Baumjohann, Edson Braafheid, Mario Gómez, Ivica Olić, Danijel Pranjić and Anatoliy Tymoshchuk. Andreas Görlitz returned to Munich after a two-year loan spell at Karlsruher SC, while Bayern declined the option to buy Massimo Oddo, who returned from loan to Milan. Tim Borowski was sold to his former club, Werder Bremen, and Lúcio left the club for Inter Milan.Zé Roberto signed at Hamburger SV after his contract with Bayern was not renewed. Just before the end of the summer transfer period, Bayern acquired Arjen Robben from Real Madrid.

In the winter transfer period, Bayern loaned both Breno and Andreas Ottl to 1. FC Nürnberg in the hopes of the duo earning first-team experience. After some quarrels with coach Van Gaal, Luca Toni moved to Roma, also on loan. Alexander Baumjohann was signed by his first club, Schalke, and Bayern loaned Edson Braafheid to Celtic in a last minute deal before the end of the winter transfer period. The Reds did not buy any new players themselves, but gave professional contracts to Diego Contento and Mehmet Ekici from Bayern II.

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