The National Museum of the Viceroyalty occupies the former Jesuit college of San Francisco Javier in Tepotzotlán, northwest of Mexico City. Before Spanish conquest, Tepotzotlán was an Indigenous political center linked to broader Nahua powers. Franciscans began early evangelization, and Jesuits arrived in the 1580s, supported in part by a local Indigenous leader, Martín Maldonado. Their institutions included a school for Indigenous boys, language training for missionaries, and a college and novitiate for Jesuit formation, making the town a major educational center in New Spain.

The complex grew around courtyards, dormitories, kitchens, refectory, library, domestic chapel, gardens, water systems, and churches. Education served religious conversion and colonial administration, but Indigenous students and workers were not passive recipients. They translated languages, created music and art, maintained buildings, and negotiated institutional demands. The college connected Tepotzotlán to Jesuit networks extending through the Americas, Europe, and Asia. Agricultural properties and donations financed scholarship and worship, while unequal labor systems sustained the community's material life.

The Church of San Francisco Javier, begun in the seventeenth century, acquired an extraordinary eighteenth-century interior. Gilded Churrigueresque altarpieces crowd the space with twisting columns, saints, angels, paintings, mirrors, and ornament designed to overwhelm the senses. Its stone façade, completed around 1760–1762, similarly turns doctrine into theatrical architecture. Craftspeople of varied ancestry made these works under elite and clerical patronage. Beside it, the older parish church of San Pedro Apóstol continued serving the town, creating overlapping institutional and community sacred spaces.

In 1767 the Spanish crown expelled the Jesuits from its dominions, seized their properties, and disrupted schools throughout New Spain. The Tepotzotlán complex later housed a college for secular clergy, including retirement and correction functions. Mexico's nineteenth-century Reform Laws nationalized church property, and political instability brought changes and periods of abandonment. Persistent rumors of buried Jesuit treasure inspired destructive searches in the early twentieth century. National monument designation in 1933 helped protect the unusually complete architecture and altarpieces.

A major restoration began in 1961, and the Museo Nacional del Virreinato opened in 1964. Collections assembled from religious institutions and national museums present painting, sculpture, silver, ceramics, textiles, furniture, books, devotional objects, and everyday materials from the colonial era. The building itself is the largest artifact, preserving educational and monastic circulation. Museum interpretation has gradually moved beyond celebrating Baroque splendor to address conquest, evangelization, caste, slavery, Indigenous persistence, global trade, and the formation of colonial society.

The complex forms part of the Camino Real de Tierra Adentro World Heritage property inscribed in 2010. Today the museum, gardens, archive, and active parish draw scholars, worshippers, residents, and tourists. Conservation must protect gilding, paintings, masonry, books, and water systems while acknowledging that sacred objects were removed from original communities and uses. Tepotzotlán offers a rare setting where institutional space and collections can be read together, revealing both the creative exchanges and the coercive structures of New Spain. Its strongest interpretation lets visitors admire artistic invention while seeing the institutional ambitions and unequal encounters that placed such beauty within a colonial college.