The Jesuits, the first evangelizers of the 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. In November 17, 1596, the first Jesuits, Father Juan de Torres, SJ and Father Gabriel Sánchez, SJ , came to Baclayon. At that time, a Catholic chapel is already existing inside the encomienda.

In 1717, Baclayon was elevated as a parish. The present stone church constructed under the Jesuits was finished in 1727. 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. Renovations on the church was done during the administration of Father Pedro de la Encarnación, OAR (1839–1854), Father Antonio Úbeda, OAR (1856–1859, 1861–1868) and Father José María Cabañas, OAR (1870–1898). The church was saved from destruction that might be brought by American soldiers in exchange for food and water in 1901. During the Second World War, the church suffered damages but was later restored. From being part of Baclayon, Balilihan, Alburquerque, Corella and Sikatuna became independent parishes in 1829, 1869, 1884 and 1914 respectively.Although it survived damages and was eventually restored, the church of Baclayon was heavily damaged when an earthquake struck Bohol on October 15, 2013.