The archaeological collection presents important medieval finds, among which the sarcophagus of the Viceroy Speciale stands out from a historical-artistic point of view, in slightly veined white microcrystalline marble, found in 1901. It presents bas-reliefs depicting the Madonna and child and another male figure who could be Saint Francis. The fortune of the Speciale family owes its origin to Niccolò Speciale: he was Viceroy of Sicily from 1423 to 1432 and created strong ties with Bianca di Navarra, reigning queen of Navarre and queen consort of Sicily and her fideles, becoming one of the major historical figures of the Sicily in the mid-fifteenth century.

The collection also includes the crucifix of the expiring Christ in incarnate stone, white and pink alabaster from the 17th century. This work, found by a farmer in the 1980s, is one of the few surviving examples of a rather dense 17th century production typical of the Trapani area, since the chalky type stone was extracted from the slopes of Mount Erice. Only the smallest crucifix preserved in the Bishop's Palace of Trapani can compete for beauty. The uniqueness of the Spiranting Christ of Noto is given by the words that Christ pronounces before expiring, highlighting his human nature: “ Deus Meus, Deus meus, ut quid delerequisti me? ".

Other important works of the collection are “the Panorama” and “The plan in prospect of the ancient city of Noto”, made by Sgroi with ink and watercolor on paper in 1887, the latter made with remarkable precision on a scale of 1: 400. Both have the emblem of the imperial eagle of Frederick II, subsequently confirmed by Ferdinand the Catholic whose victory over the Moors is testified by the white cross on a red background. The presence of the coat of arms could mean that these works are remakes of the 18th century maps made by Antonio Maria Tedeschi (now preserved in the Municipal Library), based in turn on the 17th century images of Francesco Antonio Cantone. From the same period, the Museum owns the "plan of the destroyed city of Noto" by Eng. Giuseppe Fornati (1699) who reveals the fortified walls and is of surprising technical precision.