The ground floor of this museum holds interesting exhibits on pre-Hispanic Mexico, archaeological sites, the Spanish occupation and the state's various indigenous groups. The upstairs exhibits reveal Querétaro's role in the independence movement and post-independence history. The table at which the Treaty of Guadalupe Hidalgo was signed in 1848, ending the Mexican–American War, is on display, as is the desk of the tribunal that sentenced Emperor Maximilian to death.

　　The museum is housed in part of what was once a huge monastery and seminary. Begun in 1540, the seminary became the seat of the Franciscan province of San Pedro y San Pablo de Michoacán by 1567. Building continued until at least 1727. Thanks to its high tower, in the 1860s the monastery was used as a fort both by forces supporting Maximilian and by those who defeated him in 1867.