In Candia a large number of orthodox churches existed. Most of them belonged to professional unions which devoted the churches to their protector Saints. Two large monastic complexes were built during this period, the monastery of St. Catherine and the nunnery of the Virgin Akroteriani. Though outnumbered in comparison to the catholic churches, most of the orthodox churches of Candia have disappeared, in some cases ruins are incorporated in modern constructions, a number of them were, which were turned into mosques were sold and survive in bad condition, others acquired inappropriate function and a few of them are still used for worship.

Of the most important orthodox monastery of St. Catherine only the catholicon has survived, to the NE of the metropolitan church of St. Menas, hosting nowadays an exhibition of icons and holy relics of the Cretan Archdiocese. Of the orthodox nunnery of the Virgin Akroteriani only relics of the surrounding wall survived, incorporated to the courtyard wall of the Ottoman barracks, which took its place (later it hosted the Tabaco tax office, nowadays the Ephorate of Antiquities of Heraklion).

Only a few relics are preserved of the Virgin of the Angels, the church of the Three-Martyrs, St. Marina in the Castle and St. Demetrius of the Carpenters, which preceded the modern church of St. Demetrius in the Port.

Despite the effort paid for the protection of the Venetian churches or their relics according to the Royal Decree of 1947, a large number of them was demolished in the following decades. Between them are the church of St. Nicolaos & St. John of the Merchants, demolished in 1965, St. Nicolaos in the area of the pottery workshops, known as “little hamami”, demolished in 1970, St. Irene in Delimarkou str., with colonnades and corinthian capitals, demolished in 1955, St. George Glykokarydis (Keylani teke), demolished in 1968. The church of St. John Gerakas in the quarter of Hagia Triada was demolished in 1995.