In 1529, a group of families belonging to an Otomi population called Nopala, who lived in the province of Jilotepec, set out for the area of La Cañada, in what is now the state of Querétaro. This area was inhabited by Chichimeca groups with whom the native leader of the group, named Conín, maintained a friendship and exchanged animal skins that the locals traded for salt and grains.

During the 16th century, the Spanish crown attempted to populate the territory of the former encomienda of Jilotepec, located on the Chichimeca frontier. This effort aimed to protect the road leading from Mexico City to the northern territories of New Spain.

The Hacienda de Chichimequillas is located in the municipality of El Marqués, Querétaro. It was built around 1690 by Carmelite monks who settled in the area to assist and settle the Chichimeca Jonaces and Pame indigenous people, while also providing shelter to travelers journeying along the Camino Real de Tierra Adentro to and from the mining regions of Guanajuato and Zacatecas.

The town of San Juan del Río was founded in the first half of the 16th century, as part of the jurisdiction of the mayor's office of Querétaro. It gained importance following the territorial appropriation of the Bajío region by the Spanish, becoming a significant enclave for access to northern New Spain.

It was an important ceremonial center with influences from several cultures, particularly the Toltec. Franciscan sources say that around 1632 the indigenous people continued to make offerings to the pre-Hispanic deities on these altars.