The church follows the cruciform plan under a dome that defines so much of Aegean Orthodox religious architecture — a form developed in the Byzantine period and continued with modest regional variations through the centuries of Venetian and Ottoman rule. The cupola admits a shaft of light to the center of the interior; the arms of the cross create four focused spaces around it. Inside, the wooden carved altar screen separates the nave from the sanctuary in the manner of Eastern Orthodox tradition, its craftsmanship suggesting skilled local woodworking. Frescoes cover the walls, painted when the church was renovated in 1846 at the expense of a priest and teacher named Georgios Aisopidis. That the renovation was funded by an individual — his name attached to the work in the historical record — gives the church a human scale that large institutional buildings often lack. This is a neighborhood church, in the most literal sense: it belongs to Panochori, and Panochori belongs to it.

The church holds two icons by the artist Dimitrios Halkiotis that stand apart from the conventional devotional imagery. One depicts the Apocalypse of Saint John — John the Evangelist, to whom the church is dedicated, shown in a state of profound contemplation. The second is more unusual: it represents the Virgin Mary holding the Christ child, surrounded by Elizabeth, the young John, Saint Anne, and Mary — all depicted as children, all standing rather than seated on a throne. The departure from convention is deliberate and striking. Orthodox iconography has rules about posture and hierarchy; saints typically appear enthroned or formally positioned. Halkiotis chose movement instead of stasis. The icon is noted for its vivid colors, which suggests that even within a traditional form the painter was reaching for something particular. The church was also enriched with vessels of Russian ecclesiastical art, funded by a local priest named Meletios Vayanellis who was living in Kyiv at the time — a reminder that even small Cycladic communities maintained surprising connections to the wider Orthodox world.

Kythnos is one of the quieter Cycladic islands, lacking the summer crowds that descend on Mykonos or Santorini. Its capital, Chora, sits on a ridge above the island's center — a typical Cycladic hilltop settlement, designed for visibility over the surrounding landscape and defensibility against pirate raids that were a persistent feature of Aegean life for centuries. The Church of Saint John the Theologian in Panochori represents one node in a dense network of Orthodox places of worship that covers the island; Kythnos is known for having an unusually high number of churches relative to its population. Most are small, plain on the outside, and contain within them the accumulated donations and commissions of generations of islanders — painted walls, carved screens, icons brought from distant Orthodox communities. The church near Mazarakis Square is classified as a historical monument by the Greek state, which places it within a legal framework of protection, but its real preservation has come from the ongoing devotion of the community it serves.