The parish church of Bay, Laguna was originally built by Fray Martin de Rada, an Augustinian friar-missionary who arrived with Miguel Lopez de Legaspi’s 1571 expedition. The initial structure, made of bamboo and nipa, was located along the lakeshore of what is now Barangay San Antonio and was dedicated to Saint Augustine. Bay, Laguna, which was the first capital of the Spanish-era Provincia de La Laguna, was formally established as a parish on April 30, 1578. In 1737, the administration of the parish was transferred from the Augustinians to the Franciscans. Due to frequent flooding caused by the shallowing of the lake, the church was relocated to its present site in Poblacion in 1804 under the guidance of Frs. Geronimo Hervas and Pedro Moya.

The church was severely damaged during the Japanese occupation from 1942 to 1945. In 1953, Fr. Alejandro Vermorel initiated the rebuilding of the church, leading to the construction of the present parish church. This restoration marked a significant chapter in the church's history, helping to preserve its spiritual and architectural heritage for the community.

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