The site became a parish dedicated to the Our Lady of the Pillar of Zaragoza in 1830 with the initial church building made in wood.

A convent made in stone and coral was built according to the design of Bishop Santos Gómez Marañón of Cebu under the watch of Fr.

Francisco Latorre and was inaugurated on November 17, 1907, by Manila Archbishop Jeremiah Harty.

Parish priest Julio Fernandez commissioned Cebuano artist Raymundo Francia who accomplished the artworks from 1927 to 1931.

[4] In May 2024, the Cebu Archdiocesan Commission for the Cultural Heritage of the Church requested the removal of the red-colored light-emitting diode signage installed at the Porta Sancta entrance.