He was given the title Sher Afghan Khan, by Prince Salim, Jahangir, after his meritorious actions, during a war with the Rana of Mewar . Ali Kuli Istaju, was educated under the instructions of Shah Ismail II of Safavid dynasty in Iran Like his wife, Sher Afghan was also an immigrant from Persia, who fled from Iran, to Kandahar, then in India .
He was the father of Mehrunissa's only child, a daughter, also called Mehurinissa, like her mother, though later called Ladli Begum, after she married Prince Shahryar, the fifth and youngest son of Jahangir and rival to Shah Jahan .
When he revolted against Akbar, Ali Quli sides Akbar, this led to a fall out between the two, though when Jahangir finally ascended to the Mughal throne in 1605, he excused him along with all those who favoured Akbar instead of him, and Ali Quli was made a ‘jagirdaar’ and received the region of Burdwan in east Bengal as a tuyul.
Qutbuddin, who was fatally wounded, died later in the night, causing much grief to Jahangir as he mentions in his memoirs, Tuzk-e-Jahangiri, where he also mentions his elation at the death of Ali Quli and hopes that “the blackfaced wretch will for ever remain in hell.” .
That he was killed because of the supposed love triangle, between Nur Jahan, Jahangir and Sher Afghan has been view as an assumption by many later historians, who cite the fact that if Jahangir had any such intentions, he wouldn’t have had ever bestowed upon Sher Afghan the aforesaid title, or pardoned him after he ascended the throne, or given him Burdwan .
Another historical writer, Khafi Khan mentions another extraordinary circumstance surrounding the circumstances of his death, which is said to have been related by Nur Jahan's mother. According to her, Sher Afkan was not killed by Qutbuddin's men, but, wounded as he was, managed to get to the door of his house, with the intention of killing his wife, Mehrunissa, whom he did not wish to fall into the emperor's hands. But her mother would not let him enter, and told him to mind his wounds, especially as Mehrunissa had committed suicide by throwing herself into a well. “Having heard the sad news, Sher Afkan went to the heavenly mansions.” Though this story, seems far too improbable to be true .
His tomb is today, situated, within the shrine complex of the poet ‘Bahram Saqqa’, in present day city of Burdwan or Bardhaman in West Bengal , along with tomb, Qutbuddin .
Ali Quli's daughter, who, like her mother, was named Mehrunissa, later named Ladli Begum, was married to Prince Shahryar, Jahangir's fifth son in 1620, , Shahryar went on to briefly occupy the Mughal throne at Lahore, under the maneuvering of Nur Jahan, after the death of Jahangir on October 27, 1627. He was later captured by Mughal forces led by Asaf Khan, and first blinded by the orders of Prince Dawar, was later executed by Asaf Khan, at the order of Shah Jahan, who finally ascend to the Mughal throne after executing all this remainder brothers. After Qutbuddin’s death, the next subedar of Bengal was Quli Khan (1607–1608) and when he died, Islam Khan (June 1608–died August 1613) .