Many Muslims sought shelter in the Al-Aqsa Mosque, the Dome of the Rock, and the Temple Mount area generally. According to the Gesta Francorum, speaking only of the Temple Mount area, "...[our men] were killing and slaying even to the Temple of Solomon, where the slaughter was so great that our men waded in blood up to their ankles..." According to Raymond of Aguilers, also writing solely of the Temple Mount area, " in the Temple and porch of Solomon men rode in blood up to their knees and bridle reins." Writing about the Temple Mount area alone Fulcher of Chartres, who was not an eyewitness to the Jerusalem siege because he had stayed with Baldwin in Edessa at the time, says: "In this temple 10,000 were killed. Indeed, if you had been there you would have seen our feet colored to our ankles with the blood of the slain. But what more shall I relate? None of them were left alive; neither women nor children were spared".
The eyewitness Gesta Francorum states that some people were spared. Its anonymous author wrote, "When the pagans had been overcome, our men seized great numbers, both men and women, either killing them or keeping them captive, as they wished." Later the same source writes, "[Our leaders] also ordered all the Saracen dead to be cast outside because of the great stench, since the whole city was filled with their corpses; and so the living Saracens dragged the dead before the exits of the gates and arranged them in heaps, as if they were houses. No one ever saw or heard of such slaughter of pagan people, for funeral pyres were formed from them like pyramids, and no one knows their number except God alone. But Raymond caused the Emir and the others who were with him to be conducted to Ascalon, whole and unhurt."
Another eyewitness source, Raymond of Aguilers, reports that some Muslims survived. After recounting the slaughter on the Temple Mount he reports of some who "took refuge in the Tower of David, and, petitioning Count Raymond for protection, surrendered the Tower into his hands." These Muslims left with the Fatimid governor for Ascalon. A version of this tradition is also known to the later Muslim historian Ibn al-Athir (10, 193–95), who recounts that after the city was taken and pillaged: "A band of Muslims barricaded themselves into the Oratory of David (Mihrab Dawud) and fought on for several days. They were granted their lives in return for surrendering. The Franks honored their word, and the group left by night for Ascalon." One Cairo Geniza letter also refers to some Jewish residents who left with the Fatimid governor.
Tancred claimed the Temple quarter for himself and offered protection to some of the Muslims there, but he was unable to prevent their deaths at the hands of his fellow Crusaders.
Although the Crusaders killed many of the Muslim and Jewish residents, eyewitness accounts (Gesta Francorum, Raymond of Aguilers, and the Cairo Geniza documents) demonstrate that some Muslim and Jewish residents were allowed to live, as long as they left Jerusalem.
Jews had fought side-by-side with Muslim soldiers to defend the city, and as the Crusaders breached the outer walls, the Jews of the city retreated to their synagogue to "prepare for death". According to the Muslim chronicle of Ibn al-Qalanisi, "The Jews assembled in their synagogue, and the Franks burned it over their heads." A contemporary Jewish communication confirms the destruction of the synagogue, though it does not corroborate that any Jews were inside it when it was burned. This letter was discovered among the Cairo Geniza collection in 1975 by historian Shelomo Dov Goitein. Historians believe that it was written just two weeks after the siege, making it "the earliest account on the conquest in any language."Additional documentation from the Cairo Geniza indicates that some Jews held captive by the Crusaders were able to escape when the Ascalon Jewish community paid a ransom.