Genghis Khan died in 1227, the siege of Baghdad took place in 1258 under Hulagu Khan as part of a campaign aimed at conquering the Middle East. In 1260 Hulagu withdrew the bulk of his forces to Central Asia. Historians have long believed this was to establish his claim to the Mongolian throne, the previous holder having recently died. However new documentary evidence emerged in the 1980s that Hulagu left because of logistical difficulties, the lack of fodder in the arid landscape, and the Mongol practice of withdrawing to cooler pastures for the summer. In any case his withdrawal was followed by an advance by the Mamluke Sultanate of Egypt, which met the remainder of his forces at the battle of Ain Julut, north of Jerusalem, which they won decisively.

Berke Khan of the Golden Horde had recently converted to Islam and was aghast at Hulagus destruction of Baghdad. By the time Hulagu was able to return to the Levant in 1262 he was forced to leave again, this time to meet Berke Khan in the north. This was the first major inter Mongol conflict and signalled the end of the united empire. Hulagu suffered another major defeat in 1263, this time to Berke, and died two years later.

The Ilkhanate would continue to launch invasions into the Levant but none reached the levels of the initial invasion or much success and were beset by the same problems: Mamluke resistance, hostile terrain, and inter-mongol conflict from the Golden Horde and the Chagatai Khanate (both of which were ruled by Muslims).