Typical of towns established during the Spanish colonial period, the church is located at the plaza (town square) of General Trias, which was formerly called San Francisco de Malabon in honor of its patron saint, Saint Francis of Assisi.

The first church in General Trias was established by the Franciscans when it was still a visita (sub-parish) of Cavite Viejo (now Kawit).

[3] The first stone church was erected in 1769 under the leadership of Doña Maria Josepha de Yrizzari Y Ursula, Countess of Lizarraga.

After completion, it was again consecrated on June 22, 1991, by Felix P. Perez of the Diocese of Imus in which it lies.

It is where the Banda San Francisco de Malabon, a local marching band, practiced the music of the Philippine national anthem Marcha Filipina before performing it during the Philippine Declaration of Independence from Spain on June 12, 1898, in Kawit, Cavite.