In the early 1960s, Bebey moved to France and started work in the arts, establishing himself as a musician, sculptor, and writer. His most popular novel was Agatha Moudio's Son. He also worked as a consultant for UNESCO.
Bebey released his first album in 1969. His music was primarily guitar-based, but he integrated traditional African instruments and synthesizers as well. His style merged Cameroonian makossa with classical guitar, jazz, and pop and was considered by critics to be groundbreaking, "intellectual, humorous, and profoundly sensual". He sang in Duala, English, and French. Bebey helped launch the career of Manu Dibango. Bebey released more than 20 albums over his career.
John Williams' piece "Hello Francis" is written as a tribute to Bebey: "The piece is based on the Makossa, a popular dance rhythm from Cameroon often used by Francis, and includes a quote from his piece The Magic Box and a hidden bit of J.S. Bach."