The Church of Saint Nicholas is located on the upper part of the island's western side. It had two elongated vaulted spaces (naves), with the southern one being larger in length and height than the northern one, which appears to be a later addition. It is the only building on the island that dates back to the early Venetian period, long before the Venetian fortification works.

Today, only their eastern side remains. On the southern nave's apse, there are traces of frescoes depicting the Supplication, the Christ surrounded by the Virgin Mary and John the Baptist, as well as a representation of the Annunciation of the Virgin Mary, dating back to the 14th century.

The church is the first church of the Spinalonga fortress and, during its construction, was used by the Venetians to serve the immediate religious needs of the garrison. It also serves both dogmas for a period, and at times, it is used as a powder magazine.