The Church of Our Lady of the Immaculate Conception in Baclayon is considered to be one of the oldest churches in Philippines. It is one of the best presevered Jesuit build churches in the region, although in the 19th century. Baclayon Church started the trend in Bohol of establishing parish museums. The amount of liturgical material preserved in Baclayon is impressive. The church inventory books have helped in dating some pieces. In Baclayon cantorals, a large handwritten music books was found the Misa Baclayana, a musical setting for the Mass which has been revived and is part of the repertoire of the Loboc Children's choir. Permission from the parish is needed to see the museum, which is generally locked for security reasons.
Although Baclayon was the first seat of the Spanish Jesuit missionaries, fear of Moro mauraders soon forced them to move their headquarters more inland, to Loboc. Only in 1717, Baclayon became a parish, and construction of a new church commenced. Some 200 native forced laborers constructed the church from coral stones, which they took from the sea, cut into square blocks, and piled on to each other. They used bamboo to move and lift the stones in position, and used the white of a million eggs as to cement them together. The current building was completed in 1727. The church obtained a large bell in 1835. In the Baclayon church is a dungeon, which was used to punish natives who violated the rules of the Roman Catholic Church.
Next to the church is the old convent, which also houses a small museum with centuries-old religious relics, artifacts and other antiquities, dating back to the 16th century. Included in the collection are an ivory statue of the crucified Christ looking towards heaven; a statue of the Blessed Virgin, said to be presented by Queen Catherine of Aragon; relics of St. Ignatius of Loyola, old gold embroidered ecclesiastical vestments, books with carabao skin covers, and librettos of church music written in Latin on sheep skins. Here you can also find the cuadro paintings made by the Filipino painter Liberato Gatchalian in 1859.
Despite claims that the present stone church in Baclayon is the oldest in the Philippines, evidence places the construction of the church to 1727. The belief that the church was built in 1595 may have come because of a 19th century report by the Recollects that the mission was founded in 1595; but the same report lists two other dates 1593 and 1594. The date 1595 inscribed on the church façade is a later addition.
The green and gilded altars are the focal point of the interior. They are exuberant versions of Baroque popular during the 18th century. Although the main retablo displays saints of Recollect devotion, the retablo itself traces to the Jesuits whose emblem and motto "Ad majorem Dei gloriam" surmounts the main altar. In the nave are found two benches carved in low relief. One features genre scenes: a goat tied to a tree, a coconut, nipa grove, and a man in stocks. A painting of the Ascension, Church Fathers and San Vicente Ferrer are found in the nave. These date to the 19th century.
Baclayon Church had a pipe organ installed in the 1800s but now in disrepair. The choir and organ loft are decorated with cut out designs. The painting on the stucco finish of the church is of recent vintage (1996) and does not conform to the style and period of the interior. Behind the church and convento are remnants of a fortification. Oral lore identifies some structures as horse stables, a kitchen, and a jail.