The church of Longos began as a small settlement formed by the communities of San Antonio, Abacao, and Babaye, established by St. Pedro Bautista in 1587. Initially subjected to the pueblos of Lumbang and Paete, Longos gained its first resident minister, Fray Lucas Sarro, OFM, in 1669. The church, dedicated to St. John the Baptist, was later built using durable adobe blocks to withstand the tropical climate and natural disasters. Unfortunately, much of the church’s old convent was destroyed by World War II bombs, leaving only the church building, its belfry, and sacristy intact. In 1956, Longos lost its township status and its church lost its status as a parish church when the new town of Kalayaan, Laguna, and the parish of San Juan Evangelista were established.

The church faced further challenges when a typhoon damaged parts of the structure in November 1995, but reconstruction was completed later that year. Longos was canonically re-erected as a parish by Bishop Francisco San Diego on February 13, 1996. The church was again damaged by a typhoon in 2006, but repairs were made under Fr. Elden Cabuhat and subsequent pastors. During Fr. Gabriel Ma. Delfino's tenure, additional improvements were made, including commissioned paintings and a new hall. Fr. Christian Edward Abao oversaw the installation of a parish hall and a botafumeiro. In February 2021, the parish was honored with a relic of St. Pedro Bautista, gifted from the Basilica Minore de San Pedro Bautista in Quezon City.

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