In 638 Jerusalem was assaulted and captured by Omar, Caliph of the Arab Moslems. The religious of Greek background fled the Sanctuaries and the Holy Land. The religious of Arab origins and of other ethnic/national backgrounds (Georgian, Syrian, Armenian, etc.) remained at their posts.(*4)
At first it was a period of relative freedom and tranquillity, but in the succeeding centuries the Sanctuaries suffered from earthquakes (746, 1016, 1033), from fires started by Arab Moslems (938, 966), from the partial occupation of the atrium of the Constantinian Basilica, from the destruction of all the sacred edifices and of the Rock of the Holy Sepulchre (ordered by the Fatimid Sultan Hakim in 1009), and from other profanations, killings, and persecutions. All these devastations were followed by reconstruction which was financed by the local Christians and also by the Universal Church. After the devastation at the hands of the Persians in 614, the most notable benefactors were St. John the Almoner of Alexandria (Egypt) in the sixth-seventh centuries, Charlemagne (*5) ( 814), and Constantine IX Monomachus, Emperor of Constantinople ( 1056).
The One, Universal, Catholic Church existed during the first millenium. Clergy and faithful of every race and nation were all able to pray freely at the Holy Places. In 1054 the situation changed when the Byzantine clergy separated themselves from the Catholic Church, a separation which continues to the present time.
*5 - Charlemagne exercised a true Latin protectorate over the Holy Places and over the local faithful. He sent a monthly payment of money to the clergy and local people who worked in the Sanctuaries. He also received a greater degree of liberty for Christians from Sultan Harun er-Rashid. Cf. A Couret, La Palestine sous les empereurs grecs, Grenoble 1869, 271.