The Seljuq Turks had defeated the Ghaznavids at the Battle of Dandanaqan in 1040 and entered Iran.

The Karakhanids had been able to withstand the Seljuqs initially, and had briefly taken control of Seljuq towns in Khorasan.

The Karakhanids, however, developed serious conflicts with the religious classes (the ulama).

In 1089, during the reign of Ibrahim's grandson Ahmad bin Khidr, at the request the ulama of Transoxiana, the Seljuqs had entered and taken control of Samarkand, together with the domains belonging to the Western Karakhanid Khanate.

The Western Kara-Khanids will remain a vassal of the Seljuqs for half a century, and the rulers of the Western Khanate are largely whomever the Seljuqs chose to place on the throne.

Ahmad bin Khidr had been returned to power by the Seljuqs, but in 1095, the ulama accuse Ahmad of heresy and manage to secure his execution.