The Frankish conquest of Constantinople in 1204 was a crucial point in Byzantine history, with major repercussions for all the territories in the empire. It marked the beginning of the Frankish period on Naxos, leading to its emergence as the capital of the newly created Duchy of the Aegean. Naxos Castle was built in the early 13^th century by the first Venetian ruler of the island, Marco Sanudo II, on the site of the ancient acropolis. It is now considered the most typical example of a fortified medieval settlement in the Cyclades.

The irregularly shaped wall encloses an area of ​​about 2 hectares. The original enceinte largely followed the lie of the land, so it was not necessary to create a perimeter moat or rampart. Of the sixteen towers that reinforced the wall, seven are still visible. The only one to have survived in its entirety is the Glezos or Crispi Tower near the main gate known as the Trani Porta, in the northwest of the wall, which provided the shortest route to the port. The second major gate, also called the Paraporti, was created in the south-west of the wall at the easiest point of access to the castle, linking it to the hinterland.

Multiple repairs to the walls confirm that the monument was subject to constant modification, a fact reflected in buildings from various eras in the castle interior. The Venetian period Catholic Cathedral of Naxos was built for the enthronement of the Latin Archbishop in 1244, when the Diocese of Naxos seceded from Athens and declared its independence. The church originally had three aisles, a raised central transept and a dome at the intersection; drastic alterations after 1616 ended in the current five-aisled plan.

This period saw the construction of the now ruined central tower, which served as the residence of the Venetian ruler, as well as the chancellery and the ducal administrative centre, which is now the Catholic bishop’s palace. These three buildings were laid out in the way typical of a medieval fortified city centre. The architecturally rich appearance of the castle was complemented by Panagia (Our Lady) Theoskepasti, the only Orthodox church, which predates the wall; the former Commercial School run by the Salesians, now home to the Naxos Archaeological Museum; and the Ursuline convent school complex.