The first church of Bay was constructed made of light material of bamboo and nipa by the first-ever Catholic missionaries in Laguna, the Augustinian friars of Provincia del Santisimo Nombre de Jesus.

[2] In the 18th century, the ecclesiastical administration of Bay was transferred to the Order of Franciscan Minors (OFM), with Domingo Martorel as its new parish priest on November 23, 1737.

In 1804, a structure made of bricks and wood was built under the supervision of Geronimo Hervas.

[4] When the regular clergy (missionaries) abandoned the Philippines in 1898–1899 due to the Philippine Revolution against Spain and in 1899-1903 due to the Philippine–American War, the Bay church and convent were administered by the secular clergy of the Archdiocese of Manila.

[2] In 1980s the canonical administration of Bay Church was again transferred to the newly created Diocese of San Pablo.