In pre-Hispanic times, the territory of Querétaro was part of the Central-Northern region of Mexico, inhabited by various Indigenous groups, including the Otomi, Nahua, Tarascan, Pame, and Jonace peoples.

This gallery explores the exchange networks, social organization, and political structures of the groups that settled in the Querétaro region during this period. Highlights include the establishment of early agricultural settlements along the San Juan River, the communities that occupied the Querétaro Valley and experienced the influence of the Teotihuacan state, and later, the clear Toltec presence visible in the El Cerrito archaeological site. In the Sierra Gorda, distinctive cultural traits are preserved in the archaeological sites of Ranas, Toluquilla, and San Rafael, where mining—especially of cinnabar used in ritual ceremonies—played a central role.

The Indigenous Peoples Gallery presents the native communities of Querétaro, with a focus on the Otomi (ñäñho or ñöñhö), who are primarily located in municipalities such as Amealco and Tolimán, and to a lesser extent in Cadereyta, Ezequiel Montes, Colón, and Peñamiller.

Visitors can explore cultural expressions tied to their origins, seasonal changes, the agricultural cycle, stages of life and death, ritual practices, and the symbols that sustain communal devotion and identity.

This gallery tells the story of the former "Convento Grande de Santiago de la regular observancia de San Francisco". From its founding in the 16th century, the convent was a center of spiritual and social life and a key part of Querétaro’s urban development. The gallery concludes with the founding of the Regional Museum within the Franciscan convent.

This section illustrates the blending of social groups, beliefs, and customs that gave rise to modern Mexican culture. It begins with the social restructuring that followed the Spanish conquest and the rise of the Creole population. It then explores the economic development of the region, shaped by its location on the "Camino Real de Tierra Adentro", and highlights the importance of both religious and civil colonial institutions. The gallery concludes with a section on Cadereyta and the Sierra Gorda, which was once a major administrative district (Alcaldía Mayor) and became part of the state of Querétaro in the mid-19th century.

This gallery begins in the 18th century with the Bourbon Reforms and their impact on New Spain, which introduced new liberal paradigms designed to increase wealth for the Spanish Crown. These changes set the stage for the independence movement that emerged in 1810 and culminated in 1821, seeking to forge a new identity and an independent nation.

The gallery concludes with the U.S.–Mexico War (1846–1848), a pivotal event in Mexican history marked by the loss of a vast portion of national territory.

The second part of this gallery explores the conflicts, social contrasts, and nation-building processes that shaped modern Mexico, with Querétaro playing a key role during civil wars, foreign interventions, and authoritarian regimes.

It begins with the Reform War (1857–1861) between Liberals and Conservatives, followed by the French Intervention and the arrival of Emperor Maximilian. The narrative continues through the Porfiriato and the Mexican Revolution, culminating in the 1917 Constitution. These events reflect Mexico's ongoing struggle to modernize and define its national identity.

Located in the former convent library, the Grand Hall houses sculptures, paintings, and religious furniture from the 17th and 18th centuries. It includes major works by New Spanish artists such as Luis Juárez, José de Ibarra, Juan Correa, and Miguel Cabrera—key figures of viceregal painting.

This corridor features a remarkable series of oil paintings on the life of Saint Ignatius of Loyola, displayed in semi-circular arches. The paintings are the work of Miguel Cabrera, a prominent New Spanish artist and favorite of the Jesuits in the mid-18th century.

The collection highlights the Jesuits’ influential role in shaping the education and identity of the Creole elite in New Spain and Querétaro, laying the foundation for a sense of American homeland.

The "Angels of the Passion" corridor features 14 anonymous 18th-century oil paintings from the museum’s colonial collection. Through symbols and allegories, the paintings depict scenes from the Passion of Christ, from the Last Supper to the Crucifixion, death, and resurrection.