The church, built in the 18th century, was significantly damaged when Typhoon Haiyan (local name: Yolanda) made landfall in Guiuan and struck other parts of Central Visayas on November 8, 2013.

It was handed over to the Augustinians upon instructions from the Spanish colonial government due to the Jesuits Suppression in 1768.

[2] The present stone church was dedicated to the Virgin Mary under the title of the Immaculate Conception and was built by the early Jesuits in 1718[3] and was renovated by adding a transept and baptistery during the term of Father Manuel Valverde and Pedro Monasterio in 1844.

[5] On November 8, 2013, the church along with other buildings and structures in Guiuan was severely damaged due to Typhoon Haiyan,[6] which made landfall in the town.

[7] While the roof was destroyed and the façade was damaged, the church's stone walls remain unscathed, as do the floors and the crypts.

[13][better source needed] Due to Typhoon Haiyan, all of its original retablo, roof (dated 1700s) and other church relics were damaged.