The parish covers six barangays: Damayan, Del Monte, Mariblo, Paraiso, Santa Cruz, and Talayan.

[3] When Pedro Bautista was elected custos, an official of the Franciscans, he saw the need for a secluded place where the missionaries could recharge physically, mentally and spiritually.

He found a hilly area he deemed suitable, and on February 17, 1590, then Governor-General Santiago de Vera granted the land to the Franciscan Order.

[4] The town of San Francisco del Monte was an elevated area of 250 hectares (620 acres) with thick woods, surrounded by a creek and eight springs.

The reconstruction was funded by Don Pedro Salazar, whereas the expansion of the convent was made possible by donations from Captain Domingo Ortíz de Chagoya.

[4] In 1895, the friars abandoned the place, and the following year at the time of the Cry of Balintawak, Filipino revolutionary forces occupied the church.

[5] On November 11, 1932, the church was declared its own separate parish named in honor of its founder and patron saint, Pedro Bautista.

[1] In 1989, the three-century old Baroque altars were transferred to the main sanctuary in time for the celebration of the 400th anniversary of the founding of San Francisco del Monte on February 17, 1990.

[5] On February 25, 2001, the parish church was declared an archdiocesan shrine and the name was changed to Santuario de San Pedro Bautista in view of its historical and religious significance to the Archdiocese of Manila.

The Diocese of Cubao announced on July 9, 2020, that the Holy See, on June 13 of that year,[1] had bestowed the title of minor basilica upon the parish.

A life-size image of Saint Pedro Bautista that was added during the 400th anniversary of San Francisco del Monte,[5] is enshrined at the center niche in the middle altarpiece.