The prehistoric and protohistoric section of the museum illustrates the evolution of human settlement from the first villages scattered throughout the territory to the founding of the first inhabited nucleus in the Iron Age. Among the most valuable pieces is the silver Falera, embossed, from the middle of the 1st century BC, used in the harness of horses to cover the crossings of the harness. It is adorned on the band with stylized human heads.

Among the rich sculptural furnishings of the basilica of San Salvatore, two trapezoid-shaped slabs in Proconnesian marble stand out for their refinement and precision, depicting two peacocks. While one slab has come to us intact, only a few fragments of the other are possessed. The work is rich in symbolic values, according to an iconography recurring in the early Middle Ages and of early Christian origin, which attributes to the peacock the allegorical meaning of the resurrection and immortality of the soul. The vines that surround them are traditionally brought back to the symbol of the Passion of Christ. Scholars believe that the two slabs served as a parapet for the access stairs of an ambo, located inside the church, which was suitable for reading sacred texts and reciting homilies.

Kept in the lower hall of Santa Maria in Solario, the Lipsanoteca was part of the so-called Treasury of Santa Giulia, a collection of rare liturgical objects dating back to the origins of the monastery. It is an ivory casket, rectangular in shape that was supposed to serve as a protective case for relics, as can be seen from the etymology of the name, of Greek origin, consisting of leipsanon, which means relic, and théke, or container. It was made by a workshop in northern Italy, probably Milanese, in the second half of the fourth century, under the episcopate of Sant’Ambrogio. The richness of the material, the high level of execution and the preciousness of the decoration determine the importance and rarity of this artifact.

Among the most valuable pieces of the Roman section of the museum stand out a series of imperial portraits in bronze, found in 1826 in the ruins of the Capitolium.

The monastery of San Salvatore - Santa Giulia was built on the remains of a residential area of the Roman age, now partially incorporated in the museum's visit routes with the domus dell’Ortaglia (the domus of Dionysus and the domus of the fountains). The triclinium (dining room) of the domus of Dionysus was the richest room in frescoes and is famous for the state of conservation of its floor mosaic, with the image of the god drinking a panther in the center.

Under the star-filled firmament of Ferramola, in the upper hall of the oratory of Santa Maria in Solario, the Cross of Desiderius shines, a masterpiece of Carolingian goldsmithing dating back to the 9th century AD. The Cross, which had devotional and processional functions, represents one of the rarest liturgical specimens that have come down to us both for its considerable size and for the large quantity of precious stones, 212 in total, symmetrically scattered on the wooden supporting structure, covered with a metal sheet, with the arms dilated at the ends. A work of high goldsmithing, the Cross was to represent not only the fullness of Christian devotion to Christ the Savior but also the role of the ruling dynasties, in a continuous game of cross-references between imperial power of Roman heritage and religious yearning, unearthly glory and secular symbols. The very choice to adorn the Cross with precious stones, as was done with the imperial crown, represents a clear reference to the value and power of the Church, not second to that of the Caesar.