Therefore, his reign (1672–1686) is one of regents and ministers and was marked by chronic civil war among factious nobles, independence of provincial governors, paralysis of the central administration, Mughal invasions, secret alliances but pretend hostilities with the Maratha Empire and other neighbors, and the final absorption of Bijapur into the Mughal Empire in 1686.

The prestige of Bijapur was so seriously damaged by internal disruptions that the Mughal General Diler Khan almost coerced and humiliated Sikandar.

After desperately defending his capital and withstanding the prolonged siege of Bijapur in 1685–1686, Sikandar was unable to halt the Mughal assault led by Aurangzeb.

[5] Sikandar Adil Shah was captured bound in silver chains and brought before the Mughal Emperor Aurangzeb, to whom he bowed three times.

[6] Sikandar Adil Shah was eventually buried at foot side of his spiritual teacher Naimullah Hashmi in the open yard in the New Market Place of Bijapur.