It was built between 1540 and 1550, making it the first religious place of worship in Querétaro. Unfortunately, nothing remains of these early constructions.

It belonged to the Franciscan friars and was one of the most important convents in New Spain, becoming the center of urban and economic development in the city in the 17th century.

Until the mid-19th century, the religious complex included a temple, five chapels, a cemetery, and an orchard. However, during the War of Reform, the chapels were demolished.

The San Francisco temple served as the cathedral of Querétaro between 1865 and 1922, and the remaining two-level convent building with four courtyards, showcasing sober Baroque style, currently houses the Regional Museum.

The temple has a sober facade elaborated in quarry stone in Baroque style, featuring the coats of arms of Don Luis Tovar, a benefactor of the temple, and a pair of columns in both sections topped by a beautiful relief of Santiago the Great on horseback. The monumental tower has three levels and displays Baroque ornamentation.