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After the battle of Samogarh in 1658, Aurangzeb besieged the fort and stopped its water supply from the river. Shah Jahan could not drink the well water and surrendered and Aurangzeb emprisoned him, his own father, in the fort where he lived for 8 years.

Though Shah Jahan had transfered the capital from Agra to Delhi, formally in 1638, he continued to live here, however, after his death, Agra lost its grandeur. Aurangzeb remained busy in the Deccan conflict, yet, time and again, he lived here and held the durbar (court). Shivaji came to Agra in 1666 and met Aurangzeb he diwan-i-khas in Agra Fort; he was betrayed and imprisoned, but he later escaped. Aurangzeb's death in 1707 threw the affairs of the mughal empire into chaos. The 18th century history of Agra fort is a saga of sieges and plunder. It was held by jats and marathas. The British captured it from the marathas in 1803 and converted it into an arsenal.