The band emerged from the radical West German commune scene of the late 1960s, with others in the same commune including the future founders of the Baader-Meinhof Group (the Amon Düül II band members disagreed with their violent agenda). Founding members are Chris Karrer, Peter Leopold, Falk Rogner, John Weinzierl and Renate Knaup. Their first album Phallus Dei ('God's Penis'), released in 1969, is considered a milestone in German rock history.[citation needed] They received offers to write music for films, winning a German film award, the Deutscher Filmpreis, for their contribution to the film San Domingo. Their second album Yeti was their breakthrough album in the United Kingdom.[citation needed] In 1975, they signed with Atlantic Records, and initially disbanded in 1981.

Amon Düül II's drummer Peter Leopold died on 8 November 2006. A memorial service was held for Leopold in Munich, where the remaining members of Amon Düül II sang a song for him. Leopold was replaced by multi-instrumentalist Daniel Fichelscher, for many years guitarist and drummer of Krautrock group Popol Vuh. Fichelscher is not new to the group, and in fact has had a long affiliation with Amon Düül II, having played with them as early as 1972 in Carnival in Babylon.