In June 1999, Andersson signed for Bayern Munich for approximately DM 6 million. He made his debut on 22 August 1999 in a 2–0 away defeat to Bayer Leverkusen. His time with Bayern resulted in two Bundesliga championships (in the 2000–01 championship season he scored the final and decisive goal against Hamburger SV in the last minute – his only goal for the club) as well as a DFB-Pokal and victory in the 2000–01 UEFA Champions League, despite missing his penalty in the final shootout.