He studied at the National Conservatorio Nacional de Música de Quito where in 1952 he became professor of guitar and composition.
In 1962 Bonilla founded the first guitar department at the National Conservatory of Music in Quito, Ecuador. Sought after to perform many of his own compositions which featured solo guitar and orchestra, Bonilla frequently performed with the National Symphony Orchestra of Ecuador and the Colombian Philharmonic Orchestra. Ever since the Ecuadorian National Symphony Orchestra was established in 1956, Bonilla served as principal contrabass until his retirement in 1985. He also performed a contrabass solo, Concert of Cañonery, accompanied on the piano by his brother Hector Bonilla.