Upon the conquest of Anatolia and then the Palestine and particularly Jerusalem by the Seljuks State, the Byzantine emperors increased their attempts related with the popes and these attempts caused the emergence of a movement against the Muslims in Europe gradually. Especially Aleksios Komnenos had applied to the Pope Urbain II in the year of 1091 and asked help from him. As a result of his activities, the Crusades had started that had been the greatest military operation of the history till that time. The Pope Urban II had organised a conference for the recapture of Jerusalem in the year of 1095. In this conference, he had invited all the Christians to war and he had actually affected them. The first meeting place of the Crusade army was France. Then, this army united with those who had gathered in Germany. Those who had been collected in Hungary and Bulgaria joined them on the way. The spiritual leaders of these people were two monks who were also their guides at the same time. When they came to the borders of the Byzantine, the emperor saw that most of them were composed of the troops of raiders and pillagers. He was afraid of the fact that they would ruin and despoil all the lands rather than save them. He provided their passage to the Anatolian side through the strait without any delay. The pillager Crusade group in the command of Pierre L'ermit was annihilated by Kilic Arslan's brother, Davud near Izmit. But after a short while, when the regular Crusade troops arrived under the command of counts, dukes and the knights, Turks had to retreat.

The Crusades besieged Iznik that was the capital city of the Anatolian Seljuks State. In the course of the blockade, Kilic Arslan arrived and the enemy had suffered from numerous casualties although Crusade forces were superior in respect of their number and equipment. But he could not break off the blockade. Turks who understood that the extension of the blockade would lead too much terrible casualties made an agreement with the Byzantine emperor and surrendered the delivery of the city to him (June 1097). Kilic Arslan changed the tactic of war and decided to retreat towards Eskişehir. He collaborated with Danishmend Ghazi and Eskişehir Ruler, Emir Hasan against the advance of the Crusades and he waylaid the valley that overlooked to the savanna of Eskişehir together with their forces. Both sides fought in a heroic manner in this historical pitched battle that took place in the month of July in the savanna of Eskişehir.

However, Kilic Arslan left the battlefield in order not to lose more casualties against the great superiority of the enemy and the inefficiency of the weapons of the Turks against the armoured Crusade knights. From that date on, he did not involve in any battlefield. Instead, he resorted to the tactic of deterring and wearing out the enemy through closing the water mills in the regions that the enemy was to pass, destroying the crops and evacuating the residential places. The Crusades lost great casualties in the course of passage through the Central Anatolia. Kilic Arslan encountered the Crusades again in Eregli together with Danismend Ghazi and Emir Hasan, but he could achieve any success, either. Upon the blockade of Iznik by the Crusades, Kilic Arslan moved the centre of the state to Konya.

Meanwhile, he could not send the requisite forces against Aleksios who had set in motion at the same time and the lands extending towards the line of Eskişehir-Antalya were captured by the Byzantine. Upon this success in the First Crusade, the Europeans established small Frank states in some of the Turkish-Islam countries: Urfa County (1098-1114), Antioch Princedom (1098-1268), Tripoli County (1109-1289) and Jerusalem Kingdom (1110-1268), etc. Meanwhile, Bohemond who was the count of Antioch was taken prisoner by the Danismend principality. Pursuant to this event, Kilic Arslan annihilated the Crusade troops that set in motion in the year of 1101 within the environs of Amasya and in Eregli one after the other (1102).