Jeremies moved to TSV's city neighbours FC Bayern Munich in the summer of 1998, the club for which he would play the remainder of his career. With the Bavarians he won all of his trophies, including six leagues and three domestic cups, adding the 2000–01 edition of the UEFA Champions League to which he contributed with 12 games and three goals, including one in the 2–1 semifinal win against Real Madrid (3–1 on aggregate) – he missed the final through suspension.