By the terms which were confirmed to the deputation from Famagusta which followed Mustafa Pasha to Constantinople, the Greeks were allowed to continue in the practice of the Christian religion, on condition that there should be among them no Christians of the Latin Church; the Latins were forbidden the possession of any church or house or estate of their own. Those who did remain in Cyprus were driven to conceal their faith; they attended the Orthodox churches or celebrated their rites in secret. All the dignitaries of the Latin Church had been killed or enslaved, except only the Archbishop, Philip Mocenigo, who was in Venice when the war broke out, and remained there. The monasteries had been seized by the Turks, and fell derelict; the monks disguised themselves, discarding their habits, or hid in the mountains.

But the prohibitions seem to have been gradually relaxed as peaceful relations with the western Powers were resumed. The information available on this point is chiefly concerned with Larnaca and Scala, where the representatives of western trade were to be found. At the conquest the Turks took the church of St Lazarus at the latter place, but in 1589 sold it back to the Orthodox Greeks for 3000 aspers. But the Latins were allowed to use it, or rather a chapel in the north aisle, twice a year, on the days of St Lazarus and St Mary Magdalene. The Roman Catholic colony in Larnaca had at first no parish church; for lack of one, they used the private chapels in the Consulates.