Baclayon was founded by the Jesuit priest Juan de Torres and Gabriel Sánchez in 1596, and became the oldest Christian settlement in Bohol.

When a 7.2 magnitude earthquake struck Bohol and other parts of Central Visayas in 2013, the church building sustained major damage.

The Jesuits, the first evangelizers of Baclayon, planted the first seed of Christianity in Bohol upon the request of Doña Catalina de Bolaños, mother of the encomendero of Bohol island, Pedro de Gamboa to Father Antonio Sedeno, mission superior of Leyte and Samar.

When the Jesuits were expelled in the country in 1768, the Augustinian Recollects immediately succeeded them in the late part of the same year in administering the spiritual needs of the people of Baclayon.

It is simply designed with its upper half hidden by an extended choir loft which houses an 1824 pipe organ.

[1] An inscription on the portico's pediment based on the year of construction of the façade (1875) was invisible due to church renovations.

[18] Reddish paintings on wooden panels commissioned by Father Antonio Ubeda from 1856 to 1859 can be found inside the church.

The paintings Agony in the Garden and Crowning of Thorns, also commissioned by Father Úbeda, is currently housed at the San Agustin Museum in Intramuros, Manila.

[19] A Baroque and Neoclassical pulpit made in the 1870s is located on the right side (epistle) of the church, facing the altar.

Connected to the convent is the tribuna, a private area for guests and visiting priests on the epistle side.

A silver sanctuary lamp, dated 1835 and additional details such as sconce added in 1874, is hanged on the crossing.

On the altar's center, a medallion with the anagram of the Blessed Virgin Mary can be seen which may be originally the Jesuit logo.

[3] Above the altar is a ceiling painting depicting the Last Supper and a Spanish inscription dedicated to the Virgin Mary.

[1][3][21] Inside the baptistry is an earlier image of San Juan Bautista, a baptismal font and an unusual retablo built in 1852 housing the Santo Entierro in a glass coffin and the Nuestra Señora de los Dolores in the central niche.

Several wooden chests inside the sacristy carries the flaming heart, a symbol of the Augustinian order and okir motifs.

[22] The quadrangular watchtower, which was also the church's bell tower, was left unfinished by the Jesuits when they were expelled out of the country.

Made of coral stones, it also has a bas relief of Saint Andrew with an inscription of the date the tower was finished during Father San Andrés de la Santísima Trinidad's administration, May 20, 1777.