Bonilla's professional career began in July 2008 when he signed a contract with Salvadoran national league club, C.D. Águila, after he had already joined them 2 years earlier from Dragón.
He made his professional debut on September 13, 2008, in a league match against C.D. Vista Hermosa, and scored his first goal on November 5 that same year in a league match against C.D. Luis Ángel Firpo.
On September 20, 2013, Bonilla was one of 14 Salvadoran players banned for life due to their involvement with match fixing.