It was elevated to a parish on October 31, 1690, by Father Francisco de Zamora, Provincial of the Augustinians, as a result of the increasing number of Christians in the area.

[10] In the 1980s, five early 19th-century panels depicting various saints went missing from the church's pulpit, with varying accounts attributing it to theft or an illegal sale by the parish priest.

[13] On April 1, the Cebu Provincial Board passed a motion to file charges against the National Museum and others who took custody over the panels.

[16] Aside from the panels, the church is also seeking to recover an 18th-century tabernacle which ended up in the possession of David Kamansky, the executive director of the USC Pacific Asia Museum in Pasadena, California and was later auctioned off in 2017 by the Leon Gallery for P1.4 million.

[18] The church is known for its original terracotta roof tiles and its distinct folk art or Filipino Baroque style seen predominantly on its choir screen and pulpit.

[19] Located on the central niche of the main altar is the image of Boljoon's patron, Our Lady of the Patronage, brought by Father Bartolome de Garcia from Spain in 1599.

The first floor of the church convent houses a museum containing liturgical objects such as record books, images of saints, vestments and other relics.

[22][20] Archaeological excavations undertaken by the University of San Carlos revealed several burial sites, antique jars and dishes, a necklace and a gold earring.

[23] The gold earring, the first archaeological find of its kind in a Philippine burial site, is probably worn by a person of high status and may have indicated "wealth, influence or great power".

[24] Also called the fortress or Dakong Balay (Big House), the quadrangular blockhouse was first built by Father Julian Bermejo when he came to Boljoon in 1808.

[26] The devotion to Nuestra Señora, Patrocinio de Maria began on 1599 when the Augustinians established a chapel in Nabulho, that would later be known as Boljoon, located near Carcar, dedicated to the Patronage of Mary, most Holy.

The chapel was elevated to a parish on October 31, 1690, by Father Francisco de Zamora, Provincial of the Augustinians, as a result of the increasing number of Christians in the area.

The Canonical coronation rites took place on April 23, 2022, in line with the concluding ceremonies of the 500 Years of Christianity in the Philippines.