From the time of its establishment as the fifth patriarchate of Christianity during the Council of Chalcedon (451), the patriarchate of Jerusalem formed part of the hierarchy of the Greek Orthodox Church.
In Pope Urban II’s initial plan for the First Crusade (1096-1099), he had not intended to found a Latin Church in the East. Apparently, the crusaders followed Urban’s instructions until Jerusalem was conquered in summer 1099, acknowledging the authority of the Greek Orthodox patriarch, Symeon II, because they had simply not yet found a form for the ecclesiastical order in the country. In the course of the year 1099, however, they seem to have become convinced that as the new sovereigns of the Holy Land, they needed the ecclesiastical structures familiar to them from their homes. Soon after the capture of Jerusalem, the Latin cleric Arnulf of Chocques was elected as representative of the Latin Church. When the papal legate Daibert of Pisa arrived in the Holy City at the end of 1099, shortly after the death of Urban II, the Latin patriarchate was finally authorized by the new pope. From then on, the Latins felt justified in incorporating the existing structures of the Greek Orthodox Church into the newly created Latin patriarchate of Jerusalem, arguing that the Orthodox hierarchy (in contrast to the non-Chalcedonian churches) belonged to the one church encompassing West and East. In doing so, they adopted the principle that each diocese could have only one bishop. The appointment of Latin bishops meant that the Greek Orthodox hierarchy was superseded and its clergy forced to acknowledge the supremacy of the Latin patriarch and bishops. The establishment of a Latin Church in Palestine was important in order to remain independent from Byzantium and to create a precedent for the future conquest of lands with Orthodox populations.
At least during the first years of Frankish rule, the presence of Patriarch John VIII, the successor to Symeon II, seems to have been tolerated in Jerusalem until the Latin Church was firmly established. In 1106/1107 John had to leave Palestine, and during the remainder of the twelfth century, the patriarchs of Jerusalem as well as some of the Greek Orthodox bishops spent their lives in exile in Constantinople. Soon, the main activity of the exiled patriarchs consisted in keeping alive the Orthodox Church’s claim to the patriarchate in Jerusalem. Yet Greek clergy continued to serve in the Church of the Holy Sepulchre throughout the twelfth century, and the Melkites, as the Orthodox community was known, remained loyal to the exiled patriarchs. If the authority of the Latin patriarch and his bishops was accepted, this was simply a recognition of the realities of power, but it was largely done for the sake of appearances.
In 1176/1177, the new patriarch Leontios II was sent to Jerusalem by the Byzantine emperor Manuel I Komnenos. Because of his leprosy, King Baldwin IV was not able to marry a Byzantine princess as his predecessors had done, and Manuel had sent Leontios to Jerusalem to act as his representative there. According to his Vita, Leontios was enthusiastically welcomed by the entire Melkite community. As a result of pressure exerted by the Latin patriarch, however, he soon had to leave the city again; the Latin Church obviously felt that its position was jeopardized by the presence of a Greek Orthodox patriarch in Jerusalem.
The Greek Orthodox Church profited from the conquest of Jerusalem by Saladin in 1187. The most important sanctuaries were returned to it, and between 1204 and 1206/1207 the patriarch (whose name is not known) returned to the Holy City from Constantinople. The patriarchate maintained lively contacts with the wider Orthodox world, and many Orthodox pilgrims from as far away as Serbia and Russia visited the holy places. The restoration of Frankish rule over Jerusalem between 1229 and 1244 changed nothing in this respect: the Latins were in too weak a position, and the Latin patriarchs preferred to stay in Acre (mod. ‘Akko, Israel). However, this period of relative stability came to an end when the Khwârazmians conquered the city (1244) and Patriarch Athanasios II was murdered.