Sibonga was originally a visita of Carcar starting in 1690. It was later annexed to Argao until it became a parish in 1830.

Sibonga’s first church was made of light materials. It was replaced by the present church of coral stones and bricks. Its construction was started by Fr. Juan Alonzo, who was the parish priest from 1868 to 1881. Work on the church continued until the outbreak of the Philippine Revolution in 1898. Construction continued until it was finished in 1907.

Its blessing was attended by a distinguished group of prelates including Archbishop Jeremias Harty of Manula and Bishop Thomas Hendrick of Cebu. They were accompanied by several priests from Cebu City, including Fr. Juan Gorordo, who would later return to Sibonga as the first Cebuano and Filipino bishop of Cebu.

The church’s ceiling painting was done in 1924 by Raymundo Francia, who employed a method called quadrature, a type of ceiling painting popular during the Baroque period. He painted fictitious architectural details like ceiling ribs meeting curved walls on flat surface, giving 3D illusions. The grandest feature is the seven-panel painting of the creation of the world by God.