The revolt of Turkmen (Oguz) and Harzem refugees who have recently arrived in Anatolia began in 1239 around Samsat, and spread quickly to Central Anatolia. Baba Ishak who led the revolt was a follower of Baba İlyas, the kadı (judge) of Kayseri. He declared himself Âmīr’ūl-Mu’minīn Sadr’ûd-Dūnya wa’d-Dīn and Rāss’ūl-Allāh.Although the Seljuk governor of Malatya tried to suppress the revolt he was defeated by the revolutionaries around Elbistan The revolutionaries captured the important cities of Sivas, Kayseri and Tokat in Central and North Anatolia. The governor of Amasya killed Baba Ishak in 1240, but this did not mean the end of the revolt.

The revolutionaries marched on Konya, the capital. The sultan saw that his army could not suppress the revolt, and he hired mercenaries of French origin. The revolutionaries were defeated in a decisive battle on the Malya plains near Kırşehir. The revolt was suppressed with much bloodshed. But with the diversion of resources needed to suppress the revolt, the Seljuk army was severely affected. The defence of the eastern provinces was largely ignored, and most of Anatolia was plundered. The Seljuks lost the valuable trade colony in the Crimea, on the north of the Black Sea. The Mongol commander Bayju saw this as an opportunity to occupy East Anatolia, and in 1242 he captured Erzurum.