Jesuit Missionaries in 1757 purchased a big portion of land called Hacienda de San Juan for their missions but the parish was only established in 1779 by the Franciscan friars upon gaining independence from the parochial church of Cabuyao (formerly known as Tabuco).

The church baptistery, where Rizal was baptized on June 22, 1861, by the then parish priest of Calamba Rufino Collantes and his godfather Pedro Casanas, is a recognized National Historical Landmark (Level 1).

The original baptismal records including the canonical books were lost on September 28, 1862, when Calamba Church was burned.

[4] The transcript of Rizal's baptismal certificate issued by Leoncio Lopez originally written in Spanish is shown below:[5] I, the parish priest of the town of Calamba, whose signature appears below, certify that as a result of inquiries, which with the proper authorization were made for the restoration of the canonical books (that were burned) on the 28th of September 1862 and are found in the file of baptisms, book n 1, page 49, it emerges according to the declaration of competent and sworn witnesses that Jose Rizal Mercado is legitimate son from the legitimate matrimony of Don Francisco Rizal Mercado and Dona Teodora Realonda (that) he was baptized in this parish on the 22nd of June 1861 by the parish priest Reverend Father Rufino Collantes, and his godfather was the Reverend Father Pedro Casanas.

It contained 14 life-size bar reliefs of the Stations of the Cross, a "Well of Repentance" or Balon ng Pagbabalik Loob, and a statue of John the Baptist.