He received a Fulbright scholarship and went to the United States to do postdoctoral research in the lab of Howard Schachman at the University of California, Berkeley.

He developed key techniques that are still widely used today, and used them to uncover fundamental axon guidance mechanisms.

[2][4] In 1984, Bonhoeffer became the director of the newly founded Max Planck Institute for Developmental Biology, a position he held until his retirement in 2000.

Bonhoeffer's work has been recognized with numerous awards and honors, including memberships in the German Academy of Sciences, Leopoldina, and the European Molecular Biology Organization.

The sea snail species Lophiotoma friedrichbonhoefferi, discovered by his colleague and friend Baldomero Olivera, bears his name.