During the Byzantine period, spanning from the 6th to the 15th century, Naxos harbours numerous churches scattered across plains, plateaus, and massifs. The Byzantine Churches of Naxos display a diverse range of architectural styles, including simple aisleless domed churches, barrel-vaulted churches, single or twin small free-cross domed churches, and cross-in-square domed churches.

Constructed primarily with stone, they are characterised by their modest size and uncomplicated designs. The churches' interior decorations showcase captivating paintings, which, although possessing a provincial charm, demonstrate a remarkable level of artistic skill and variety. Notably, some churches feature abstract decorative elements. The decorative themes often incorporate geometric patterns and depictions of animals, reflecting the influence of the iconomachy period. It is worth mentioning that the construction of Orthodox churches continued during the Venetian rule, particularly in the second half of the 13th century and the first half of the 14th century.

To get a glimpse of Byzantine Naxos, visitors can explore several notable churches:

Church of Panagia Drosiani

Located on the road from Chalki to Moni, Panagia Drosiani is one of the island's most remarkable churches. Dating back to the 6th century, it is believed to be Naxos' first Christian building, adorned with rare wall paintings from the 8th century. Notably, Panagia Nikopios is a prominent depiction within the church, portraying Madonna and Jesus together. Madonna's face is particularly striking, exhibiting delicate and idealised beauty.

Church of Panagia Protothroni in Chalki

In the village of Chalki, visitors can discover an important example of Byzantine architecture. It showcases successive layers of wall paintings from the 19th-10th centuries and the 12th-13th centuries. Experts suggest that the church dates back to the 9th-10th centuries and was constructed atop an ancient temple. Other noteworthy churches in the area include Aghioi Apostoloi Metochi (Chalki), Aghios Ioannis Theologos in Kerami, Panagia Damiotissa in Kaloxylos, and Aghios Georgios Diasoritis near Chalki.

Church of Aghia Kiriaki in Apeiranthos

Situated at the end of an ancient stone-paved path, the two-aisled Church of Aghia Kiriaki boasts 9th-century abstract decorations.

Church of Aghios Mamandas

Located near Kato Sangri, this cross-in-square domed church dates back to the second half of the 10th century. Its interior is adorned with remarkable sculptures, and a carved inscription associates the church with Bishop Leon.

Church of Panagia Archatos

Situated in the area of Achatos, this two-aisled cross-shaped church contains preserved wall paintings from the 13th century.

Monastery of Christ Fotodotis

Nestled in the mountains, the Monastery of Christ Fotodotis in Danakos offers panoramic views of Mount Zas and the eastern coasts of the island. The monastery's founder is subject to various legends, with some attributing its construction to a Byzantine princess and others to Empress Irini or her son Alexios Komninos in the 12th century following a victorious expedition.