The museum complex is located in the church and convent of San Francesco. From a monumental cloister you enter the church, where traces of frescoes dating back to the 14th-16th century are preserved. The Pinacoteca houses, among the most prestigious works, the 13th century wooden group representing the Deposition and the banner by Bartolomeo Caporali depicting the Madonna della Misericordia. The visit is enriched by the “Talking Drum” ethnographic museum which exhibits the collection curated by Enrico Castelli, an Africanist anthropologist from the University of Perugia who has been studying African cultures for about thirty years.

The church represents the central nucleus of the museum, preserving inside numerous frescoes mainly of a votive nature. The surviving passages of the oldest frescoes, datable to the second half of the fourteenth century, suggest that a large decorative intervention was undertaken immediately after the construction of the church. The highest results of the decoration of the church, however, belong to the following century, when the building became the family church of the Fortebracci who generously contributed to its embellishment, providing it with altars, furnishings and paintings. In the church there are also valuable wooden works, such as the counter of the magistrates with inlay motifs inspired by the "grotesques", the wooden choir and the pulpit.

The collection of the Pinacoteca includes a group of paintings dated between the sixteenth and eighteenth centuries, coming from the churches of Montone, witnesses of the village's relations with Perugia and Città di Castello. The wooden Deposition is one of the most valuable works. The four components of which it is composed were perhaps part of a group of five figures, with Christ, the Virgin, St. John the Evangelist, St. Joseph of Arimathea and Nicodemus. Among the seventeenth-century paintings, the most notable is the one depicting Saint Anthony of Padua with the Child.

Finally, the new archaeological section collects evidence of a discovery of a Roman villa near Santa Maria di Sette from the 2nd century AD.