Period of the Mameluks
The defeat of the crusaders by the Mameluks of Salah-ed-Din in 1187 at the heights Of Hattin, close to Tiberias, turned over Jerusalem again in the hands of Islam, even though the final departure of the Crusaders from the Holy Land came after their defeat at Ptolemaide in 1291. Salah-ed-Din, keeping, out of respect, the decree of Omar Hattab, turned over all the shrines to the Greeks. However some of his high level administrators turned over some shrines to the monophysite Copts and Abessynians (Ethiopians). The attitude of the Mameluks toward the Greek Romean Patriarchate changed at the beginning of the 14th century and long lasting persecutions started against the Christians within which framework, the Church of the Resurrection, later during the time of the Patriarch Joachim (1431) almost became an Islamic mosque. Around 1334 the Franciscans appeared in Jerusalem and settled on the hill of Sion, while in parallel the presence of the Jacobites and Armenians was strengthened. These were offset by the arrival of many Georgians and Serbian Orthodox monks which strengthened the Greek Orthodox Hagiotaphitic (Brotherhood of the Sepulchre) presence but not always without complications. The Greeks turned over the Monastery of the Holy Cross to the Georgians, while to the Serbs they turned over the Holy Monastery of the Archangels, a metohion of the Lavra of Saint Savva.
The collapse of Constantinople to the Turks (1453AD) and the consequent complete loss of its official political protection, marked the beginning of new persecutions. Patriarch Athanasios 4th, having travelled to the City (Constantinople) succeeded in the issuing of a Sultanic decree (hati serif) by Mohammed the Pillager (in 1458) which averted the danger of destruction of the shrines and the loss of the rights of the Orthodox on them. Patriarch Gregory 3rd (1468-1493) also later did likewise succeed in the issuing of a new decree by the Pillager. The Greek clerics were plagued by terrible poverty while their turning to the Pillager worsened their relationship with the Mameluks and of course with the Latins.