As the capital of Crete for many centuries, Heraklion developed into an important religious centre with numerous churches, monasteries and convents. During the Venetian period in particular, Orthodox and Catholic churches, monasteries belonging to different religious orders and important ecclesiastical schools were founded in Candia.

During the Second Byzantine Period, the Church of Saint Titus served as the seat of the Orthodox Archbishop of Crete. After the arrival of the Venetians, it became the Catholic cathedral and the seat of the Latin Archbishop. The present building was constructed as a mosque during the Ottoman period and returned to Christian worship following the population exchange.

Saint Catherine of Sinai was an important centre of education and ecclesiastical art. During Venetian rule, a renowned school operated here, teaching theology, philosophy, ancient Greek literature and painting. Today the church houses the Byzantine Collection of the Archdiocese of Crete, including important icons, religious treasures and works associated with the Cretan School of icon painting.

Other notable religious monuments include the Basilica of Saint Mark, once the Venetian cathedral, the Church of Saints Peter and Paul of the former Dominican monastery, the small Church of Saint Minas and Pantanassa and the newer Cathedral of Saint Minas, one of the largest churches in Crete.

Following the Ottoman conquest of Candia in 1669, many Christian churches were converted into mosques and monastic buildings were given new uses. Some monuments were returned to Christian worship after the departure of the Muslim population, while others now serve as museums and cultural venues.

Many important religious buildings have not survived. Particularly during the first decades of the 20th century, old churches, minarets and monastic remains were demolished as the city expanded and modernised. The monuments that survive today provide valuable evidence of the Byzantine, Venetian and Ottoman history of Heraklion.

Heraklion is now the seat of the Archdiocese of Crete. The Church of Crete has a semi-autonomous status and remains under the canonical jurisdiction of the Ecumenical Patriarchate of Constantinople.