It was severely damaged when a 7.2 magnitude earthquake struck Bohol and other parts of Central Visayas on October 15, 2013.

[6][7][8] Fire destroyed the original wooden church in 1638; it was later reconstructed by the Jesuit priest Jose Sanchez.

[9] After the Jesuits were expelled from the country in May 1768, the Augustinian Recollects assumed the administration of the parish and the church that November.

[12] The church complex was a candidate for UNESCO World Heritage Sites of the Philippines, under two distinct categories.

[4] On May 24, 2021, the church was declared as the Diocesan Shrine of Our Lady of Guadalupe in Extremadura, the same day that it was also affiliated with the Papal Basilica of Saint Mary Major in Rome.

[9] Major renovations were undertaken by Augustinian priest Father Aquilino Bon, including the addition of a portico to the façade (1863–1866) and re-roofing with tiles (1873).

[9] Father José Sánchez, OAR, added stone buttresses to the walls (1891–1893) and side porticoes (1895–1896).

[21] The interior of the church is adorned with ceiling paintings by Canuto Avila and his sons, Ricardo and Ray Francia, created from May 1926 to July 1927, and retouched by Cris Naparota in 1995.

[21] The inner baroque façade, which is part of the 1734 church built by the Jesuits, is decorated with pilasters, capitals, blind niches and volutes.

[21][22] It is patterned after the San Ignacio Church in Intramuros, with two levels, a triangular pediment, and two narrow octagonal bell towers on each side.

[20] Behind the walls of the retablo mayor are the remains of the former Jesuit altarpiece, a bas-relief of Saint Ignatius Loyola and St Francis Xavier dressed as a pilgrim.

The larger altar on the right side currently houses the image of St. Francis Xavier as preacher on the topmost level.

[24] The tomb of Father Aquilino Bon and other Recollect priests who served Loboc are also on this side of the church.

The smaller retablo, also of the same style, houses the images of Saint Joseph with the child Jesus, and St Isidore the Laborer on the lower and upper level, respectively.

It was built parallel to the transept and was an unusual three-storey structure, with a two-storey outdoor gallery (called a volada) and thick walls.

[10] A detached four-storey bell tower was built near the riverbanks by the first Augustinian Recollect priest of Loboc.