The purpose of the Crusades was for Christians in Europe to retake Jerusalem in the name of Christianity from the Jews and Muslims. In fact, Pope Urban II told those Christians who were to fight that if they died during the Crusades, they would have their sins forgiven.
Before those in the first Crusade reached Jerusalem, they had already spent dozens of months fighting their way across Europe. By the time they arrived in Jerusalem, the Muslims and the Jews had been warned and were prepared to fight. As the crusaders entered into the city, Jews and Muslims fought together to defend themselves. When they sought refuge in synagogues, crusaders set many of these edifices on fire. Many of those Muslims and Jews who did not die in the fighting were sold into slavery. The Muslim and Jewish community of Jerusalem was greatly diminished for many years.
Jews and Muslims alike were killed in Jerusalem during the First Crusade. The Christian knights came under order of the Pope to free Jerusalem, which was considered to be the Holy City for all three religions. These Christian soldiers killed whoever was in their way, and although they killed less of their fellow Christians than in the later Crusades, there were still many casualties of Christians at the hands of other Christians.
There is little doubt that crusading armies brought a certain level of religious fervor that would result in many atrocities throughout the First Crusade. The crusade itself was called partly as a means to rejuvenate western Christendom, and the relatively diverse crusader armies united themselves under a religious banner for the infamous Siege of Jerusalem - the Holy City -in 1099. Here, many contemporary accounts point to the massacre of both Jews and Muslims at the hands of Christian forces. While we have no positive number of the amount of Jews and Muslims killed (contemporary sources tend to have a flair for the dramatic), we can reasonably assume that such massacres were not uncommon and were indeed barbaric. For reference, see the Rhineland massacres of 1096 for examples of antisemitism demonstrated by crusader armies.
It is important to understand to volatile political situation of Western Europe (and indeed the Middle East) at the launch of the First Crusade. Tensions and disputes between rulers in Europe often bubbled over into the daily life of the crusader armies, and indeed into the politics of the Levant region itself. The crusades were very much a medieval phenomenon in which religious idealism reared its ugly head on both sides of the conflict.
Asbridge, Thomas (2004) The First Crusade: A New History
Madden, Thomas (2005) New Concise History of the Crusades
Many Jews and Muslims were killed during the first Crusade; approximately ten thousand Jews were killed during this time. Muslims and Jews (who worked together in many instances to defend their land) found their villages burned and their families slaughtered. Christian knights were determined to “free” the Holy City from non-believers.