The Fatimids were Shi’ite rulers (as opposed to the Umayyads and the Abbasids, who were Sunnis), from Egypt. In 970, the Fatimids conquered the Land of Israel from the Abbasids, but the Abbasid Empire continued in existence.

In the eleventh century an earthquake damaged the walls of Jerusalem, which until that time had included the City of David and Mount Zion. The Fatimid rulers of the city restored the walls along a smaller line, excluding the City of David and the southern part of Mount Zion; this is the line the wall follows to this day. Of particular note is the Fatimid ruler Al-Hakim, who persecuted non-Muslim minorities, especially Christians. He destroyed their churches, including the Church of the Holy Sepulchre, which was only restored during the time of his successors. In 1071, the land was conquered by the Seljuk Muslims, a rising power that defeated the Byzantines, who threatened the Islamic world. The Seljuks ruled the land until 1098, when the Fatimids returned for a number of months before the Crusader invasion of the Middle East.