The Church of St. John the Theologian in Margarites is located at the southwest side of the village. It is a single-room vaulted temple and its interior bears traces of frescoes and an impressive stone iconostasis (icon shrine). On each side of the temple there are three blind arches. The entrance doorway is carved from limestone, while the upper parts of the interior walls bear holes used for improving the acoustics of the church.
The church was originally much bigger as it is surrounded by derelict outbuildings, of which three apses are preserved. The frescoes date back to 1383, as stated in a surviving inscription.