The Sultan regarded the Ecumenical Patriarch of the Greek Orthodox Church as the leader of all Orthodox, Greeks or not, within the empire. The Patriarch was accountable to the Sultan for the good behavior of the Orthodox population, and in exchange he was given wide powers over the Orthodox communities, including the non-Greek Slavic peoples. The Patriarch controlled the courts and the schools, as well as the Church, throughout the Greek communities of the empire. This made Orthodox priests, together with the local magnates, called Prokritoi or Dimogerontes, the effective rulers of Greek towns and cities. Some Greek towns, such as Athens and Rhodes, retained municipal self-government, while others were put under Ottoman governors. Several areas, such as the Mani Peninsula in the Peloponnese, and parts of Crete (Sfakia) and Epirus, remained virtually independent. During the frequent Ottoman–Venetian Wars, the Greeks sided with the Venetians against the Ottomans, with a few exceptions. The Orthodox Church assisted greatly in the preservation of the Greek heritage, and adherence to the Greek Orthodox faith became increasingly a mark of Greek nationality.
The emblem of the Ecumenical Patriarch of Constantinople.
As a rule, the Ottomans did not require the Greeks to become Muslims, although many did so on a superficial level in order to avert the socioeconomic hardships of Ottoman rule or because of the alleged corruption of the Greek clergy. The regions of Greece which had the largest concentrations of Ottoman Greek Muslims were Macedonia, notably the Vallaades, neighboring Epirus, and Crete (see Cretan Muslims). Under the millet logic, Greek Muslims, despite often retaining elements of their Greek culture and language, were classified simply as “Muslim”, although most Greek Orthodox Christians deemed them to have “turned-Turk” and therefore saw them as traitors to their original ethno-religious communities.
Some Greeks either became New Martyrs, such as Saint Efraim the Neo-Martyr or Saint Demetrios the Neo-martyr while others became Crypto-Christians (Greek Muslims who were secret practitioners of the Greek Orthodox faith) in order to avoid heavy taxes and at the same time express their identity by maintaining their secret ties to the Greek Orthodox Church. Crypto-Christians officially ran the risk of being killed if they were caught practicing a non-Muslim religion once they converted to Islam. There were also instances of Greeks from theocratic or Byzantine nobility embracing Islam such as John Tzelepes Komnenos and Misac Palaeologos Pasha.
Byzantine historians noted the liberal and generous nature of Ottoman Sultans. Bayezid I, according to a Byzantine historian, freely admitted Christians into his society while Murad II set out reforms of abuses that was prevalent under Greek rulers. Persecutions of Christians did nevertheless take place under the reign of Selim I (1512-1520), known as Selim the Grim, who attempted to stamp out Christianity from the Ottoman Empire. Selim ordered the confiscation of all Christian churches, and while this order was later rescinded, Christians were heavily persecuted during his era.