In the 1984 summer, aged almost 29, Eder signed with FC Bayern Munich, for 150,000 Deutsche Mark. During his four-year spell, he never played in less than 32 league games, going on to win three consecutive national championships. In the 1986–87 season, he appeared in 44 official games, including nine in the season's European Cup – he played the full 90 minutes in the final 1–2 loss against F.C. Porto in Vienna.