The history of the church of Baclayon dates back to the time when the first Spanish missionaries who hailed from Cebu, Fr. Juan de Torres and Fr. Gabriel Sanchez, settled in the area on November 17, 1596 and a visita was erected soon after.
The first church that the natives of the area constructed was built of bamboo with thatched roofing. It was then the residence of their Superior General and called the “Residencia” or center of the Bohol missions. The mission spread to the hinterlands of Bohol and in 1596, Fr. Juan de Torres established another settlement in Loboc.
But the peace and order situation in this coastal settlement was often broken by raids done by Moro invaders. After a vicious attack on the settlement, the Jesuit Missionaries moved the center of their missionary activities to the inland village of Loboc on October 26, 1600.
Loboc became a parish in 1602 and from that time until the 18th century, it played host to the “Residencia”. Meanwhile, life in the Baclayon settlement went on as usual. Steadfast in their faith, the people did not join their Bohol comrades in raising arms against the Spanish conquistadors during the Tamblot or Diwata Uprising in 1621.
Finally, in 1717, the settlement was raised to the status of a parish and construction of a new and sturdier church and a 21meters high bell tower began. Through forced labor, 200 natives worked on the church until its completion in 1727.
Some of the artisans were assigned to get the coral stones far off in the sea. Others hauled them to the site while the skilful ones cut the coral stones into square blocks. The square blocks were then lifted and moved into position using bamboo poles and eventually piled like bricks. The white of a million eggs were used with lime to cement the coral stones together.
Somewhere underneath the Baclayon Church is a dungeon where natives who violated the rules of the Spaniards and of the Roman Catholic Church were imprisoned. Beside the back portion of the church was built a convent which now houses a museum containing religious relics, artifacts and other antiquities dating back to the 16th century.
Because the foundation of the church was laid in 1717, this makes Baclayon Church the second oldest stone church in the Philippines; second to that of the San Agustin Church located in Real Street, Intramuros, Manila, whose foundation is said to have been laid in 1571. The church was then dedicated to the Our Lady of the Immaculate Conception.
Later in 1835, a large bell was installed and in the 19th century, the Augustinian Recollects added the front facade of the church with its three arches and a number of stone buildings which now surrounds the church. All these are still standing at present making it the most preserved church in Bohol.