Gerster played youth football in Bavaria, playing for his hometown club FC Kempten and later FC Augsburg, before joining Bayern Munich in 1994. He progressed through Bayern's reserve team, and was promoted to the first team in 1996, making his Bundesliga in March 1997 as a substitute for Marcel Witeczek in a 2–0 defeat to Arminia Bielefeld. He made a further eight appearances for Bayern - all as a substitute - seven came in the League and one against IFK Göteborg in the group stage of the 1997–98 UEFA Champions League. During his time at Bayern, Gerster won a League title and a Cup and also represented Germany, being named in the squad for the 1995 FIFA World Youth Championship in Qatar, and making fourteen appearances for the Germany under-21 team.