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During the period of Turkish rule, the Ecumenical Patriarchate used its position within the [[Ottoman empire]] to help the Church in Crete by bringing many of the monasteries under the protection of the Patriarchate as stavropigial institutions. This practice began under the first metropolitan under Turkish rule, Neophitos Patellaros, who from 1654 transferred many of the largest and most wealthy monasteries including Arcadi, Arsanios, Holy Trinity of Tzagarolon, Holy Virgin of Gdernetos, Chrissopigis, and Jerusalem of Malevizi.
As agitation for Greek independence gained popular support, the people of Crete revolted against the Turks. In retaliation on [[June 24]], 19211821, the Turks conducted a massacre in Herkalion that is remembered by the populace as ‘’o megalos arpentes’’ (the great ravage). Among the victims were Metropolitan Gerasimos Pardalis, and five of his bishops: Neofitos of Knossos, Joachim of Herronissos, Ierotheos of Lambis, Zacharias of Sitia and Kallinikos, and the titular bishop of Diopolis. The [[see]] of metropolitan remained vacant for the next two years until the sultan consented, in 1823, to the consecration of Kallinikos of Anchialos as the Metropolitan of Crete. At the same time the bishopric of Knossos was abolished and became part of the metropolis.
During the time of Metropolitan Meletios A’ Nikoletakis (1830 to 1834) the structure of the Metropolis changed greatly. Bishoprics were merged to make five bishoprics. In 1862, the bishoprics were re-established as before except that Knossos remained part of the metropolis. Later, Metropolitan Dionissios Chanritonides began construction of a new, larger Cathedral of St. Minas. This cathedral was completed and consecrated under the last metropolitan to rule under Turkish rule: Timotheos Kastringannakis (1870 to 1898). The consecration took place on [[April 18]], 1895.