Throughout Venetian rule, the Church of Crete came under the influence of both East and West. Since the political stance of the islanders was bound up with their particular faith, the Venetians attempted to isolate Crete from the Orthodox Patriarchate. They thus forbade the ordination of priests, abolished the Orthodox dioceses and sequestrated Orthodox Church property. Roman Catholic bishops were installed to replace their Orthodox counterparts, and senior clerics (known as protopappades) were placed in charge of the Orthodox clergy.

Relations between the Catholic and Orthodox faithful were to prove one of the major thorns in the side of Venetian rule, and one with grave political repercussions. The Cretans fiercely withstood Catholic propaganda.

Led on by their common language, common faith and common ancestry, the islanders identified with other people in the Byzantine Empire. In this way, their stance on religious matters became linked to the idea of national consciousness.