The Church of Crete is semi-autonomous (self-governing) under the jurisdiction of the Ecumenical Patriarchate of Constantinople.

The Church of Crete has been self-governing since late Ottoman times.

In 1962, the Ecumenical Patriarchate elevated the island's bishoprics to metropolises, and in 1967, the Metropolitan of Crete was promoted to Archbishop.

The patriarchate nominates the island's presiding bishop from a list of three Cretan bishops prepared by the Greek Ministry of National Education and Religious Affairs, but the church's affairs, including the nomination of the other bishops, are otherwise handled by the Holy Provincial Synod of Crete.

The link with the Patriarchate ensures less opposition to ecumenism than generally expressed in the mainland Church of Greece.