The Jesuits came to Tepotzotlán in 1580 to work with the indigenous population. As a result, the first institution they founded was the Seminary of San Martín, devoted to educating the sons of indigenous nobles. Then a school of languages was established, where the Jesuits learned Otomí, Nahuatl, and Mazahua. The third foundation was the Probation House where young people who wished to enter the Society of Jesus did their religious studies.
In this way, a single building served various educational institutions, but the Jesuits oversaw the different spaces in accord with the functions carried out in each of them. The architectural complex was composed of five patios, a garden, two mills, a guest quarters, and a church. The origin of this large complex was a simple house, which through time was transformed into 10,000 square meters of construction with the support of the benefactors and the institution’s resources.
On July 4, 1767, the Jesuits living in the school had to vacate it under the orders of King Charles III who had decreed the expulsion of the Jesuits in the New World. In 1777, under the instructions of Archbishop Alonso Núñez de Haro y Peralta, the creation of the Seminary College of Tepotzotlán was approved. It functioned in this building until the mid-nineteenth century. In 1870 the Jesuits returned to Tepotzotlán, but were forced to leave once and for all in 1914 as a result of the political turmoil in the country.
Later the building was declared a national monument and in 1963 the Instituto Nacional de Antropología e Historia (National Institute of Anthropology and History; INAH) began restoration work to house the National Museum of the Viceroyalty, which was inaugurated on September 19, 1964.