Starting in the 1960s, Mangelsdorff's style shifted toward the avant-garde; he developed a method of producing multiple sounds with the trombone and frequently played and recorded solo. He performed in several long-running groups and co-led the German-French Jazz Ensemble. In the 1990s, he became music director for JazzFest Berlin.
Mangelsdorff recorded with pianist John Lewis, drummer Elvin Jones, trumpeter John Cherry, and guitarist John Scofield, among others.