The conversion of the Orthodox population of his realm was never a goal of Mehmed II. or his successors so he kept the structures of the Orthodox church intact.

Interestingly, the city of Constantinople didn't have a patriarch that was generally recognized when it was conquered by Mehmed in 1453. That was because of the efforts of emperor Constantine XI. to mend the schism between the Orthodox and Latin churches in order to aquire some help from the Popes for his beleaguered city. The union with Rome wasn't at all popular with large parts of the Orthodox clerus. So already in 1450 the pro-unionist patriarch Gregory III. had to abdicate and went into exile in Rome. When Mehmed II. took Constantinople order had to be restored. The union with Rome was now more or less off the table because its main advantage, help against the Ottomans, had become obsolete. So now Mehmed could install a prominent opponent of the union on the patriarchal seat. This man was Gennadios II. Scholarios. The ecumenical patriarch now became the official spokesperson (ethnarch) for all Orthodox subjects of the Ottoman monarchy.

Because the Hagia Sophia was to be converted into a mosque the new patriarch had to move his seat to the second most important church of the city, the Church of the Holy Apostles, the burial place of many emperors and patriarchs. Only a few years later it moved again when that church was destroyed and gave way to the Fatih Camii, the burial mosque of Mehmed II. The new seat now was the monastery of Pammakaristos in the north-west of the city. When that was converted into a mosque as well at the end of the 15th century the patriarchate moved one last time into the district of Phanar at the Golden Horn, which until today is the main focus of Orthodox Greek settlement in Istanbul.