The museum encapsulates the history of the city of Todi, showcasing and cataloging objects discovered in the city and its surroundings. Among the notable items are a marble slab from the 10th-11th century featuring the effigies of San Fortunato, Christ the Redeemer, and Saint Cassian. The museum also displays a wooden model attributed to Ventura Vitoni, depicting the Temple of Consolation, built in 1571, as well as the saddle of Anita Garibaldi.

The archaeological section features Greek-style ceramics, which testify to the commercial exchanges between Todi and Orvieto, along with bronze objects, including a copy of the famous Mars of Todi statue, dating back to the 5th century BC, discovered in 1835 near the Convento di Montesanto (the original is housed in the Vatican Museums in Rome).

The numismatic section presents pre-Roman, Greek, Roman, Ostrogothic, Byzantine, and medieval coins. The ceramics section, decorated from the 1600s to the 1900s, includes works by Pier Paolo Sensini and Ignazio Mei.

Finally, the museum also features a textile section and a Pinacoteca, where visitors can admire The Coronation of the Virgin by Giovanni di Pietro, known as lo Spagna (a disciple of Perugino), and works by Ferrau Fenzoni, known as Il Faenzone, who worked extensively in Rome for Pope Sixtus V.