During the reign of Akbar's successor Jahangir, he played a key role in the suppression of prince Khusrau's rebellion, and later governed the provinces of Gujarat and Punjab.

[6] In the Mughal court there was a movement of Naqshbandis who had been trying to garner power in the hopes of supplanting the religiously erratic Akbar with a more stable and orthodoxly Muslim emperor.

Du Jarric among the Jesuits at court described that Shaykh Farid had been sent as a representative of the orthodox faction to promise support of Prince Salim (future Mughal Emperor Jahangir), "provided that he would swear to defend the law of Mahomet".

After Khusrau was later captured, Jahangir awarded Shaikh Farid the title 'Murtaza Khan' for his actions, and his rank was increased to 6000 horses.

[15][13] Shaikh Farid's tomb is located in Malviya Nagar, Delhi, near a caravanserai constructed by him named Serai Shahji.