Before the Spanish Conquest of Mexico, the land originally belonged to an Aztec lord and was the site of a pyramid shrine to the god Huitzilopochtli. This shrine was eventually destroyed by the Franciscan friars under Pedro del Monte. They Christianized the site using the stones and the foundation of the shrine to build a small church and house for themselves. The current structure was built to replace the smaller house and church near the end of the 17th century. Diego del Castillo and his wife, Elena de la Cruz sponsored the construction which was completed under architect Cristobál Medina Vargas. Work was completed in 1678, and designed to house thirty monks. The Aztec remains lay forgotten until excavation work in the late 20th century uncovered the pyramid foundation, Nahua sculptures, and human remains. Some of these are on display at the museum.