Muhammad Ismail was with the Emperor during the 30-year-long Deccan Wars with the Sultanates of Golconda and Bijapur and the Marathas. He was sent by the emperor against the Maratha stronghold of Raigarh against Raja Ram Bhonsle. But the widow of Sambhaji, Yesubai and her minister Ramchandra Bavdekar Pant Amatya sent young Raja Ram Bhonsle to the stronghold of Pratapgarh through Kavlya ghat from where he escaped to the fort of Jinji in present-day state of Tamil Nadu arriving on 1 November 1689. Muhammad Ismail was given the title Itikad Khan and sent along with the naval commander Siddi Qasim Yaqut Khan besieged Raigarh in March 1689 till 19 October 1689 when Yesubai and her minister Ramchandra Bavdekar Pant Amatya surrendered on the promise that Itikad Khan swear on the Quran that he would protect her and Shahu II against any cruelty. Itikad Khan did so. But before Yesubai could surrender Raigarh, she was forestalled by the military governor, Suryaji Pisal. He had, or pretended to have claims to be Deshmukh or hereditary revenue officer of Wai. He sent word to Itikad Khan that if he promised to get him made Deshmukh, he would throw open the gates of Raigarh. Itikad Khan gave his promise and secured the fortress 19 October 1689. Thus with the capture of Raigarh, the heir apparent Shahu II and his mother Yesubai were also taken captives.
Itikad Khan kept his word both to Yesubai and to Suryaji Pisal. The latter Itikad Khan took to the emperor and asked him to give Suryaji Pisal the price of his treachery. Emperor Alamgir received him graciously, and thus he was made Deshmukh of Wai; but he lived to regret his infamy. 18 years later Shahu II returned from Delhi. One of his first acts was to put to death Suryaji Pisal and several of his family in revenge for the long captivity which he had himself endured.
On the capture of Raigarh all that remained of Shivaji's treasure, all the records of the Maratha government, the royal horses and elephants with their state trappings, and the golden throne made by the great king for his coronation, fell into Itikad Khan's hands. So did a mistress of Sambhaji and his natural son Madan Singh. As a reward for this splendid success Itikad Khan was given the title of Zulfiqar Khan and ordered to reduce Panhala Fort. Siddi Qasim Yaqut Khan was rewarded by the grant of the Ratnagiri districts of Anjanvel and Sindhudurg.
The Maratha commandant of Panhala Fort was Ghatge of Kagal. He surrendered to Zulfiqar Khan in April 1690. Zulfiqar Khan was now sent on the most enduring task of his and the Mughal Empire's legacy in South India, to besiege Jinji Fort. In the first siege of the fort from 1690-1695 CE. he along with his father Asad Khan and Prince Muhammad Kam Bakhsh failed to capture the fort. Disagreement with the young prince and the mutiny of the Mughal artillery were the reasons for the failure of the siege on top of the Maratha insurgency. Zulfiqar Khan settled the matter with an armistice and moved some troops to Madras with himself moving to Vandavasi. There he found refuge and a new ally in the British East India Company. Fort St. George's Governor Elihu Yale (the founder of Yale University in the United States), helped in all possible ways in return obtains a kaul from Vizier Asad Khan confirming the existing grants for the factories of Madras, Masulipatnam, Madapallam, Vizagapatam, Fort St. David, Cuddalore, and Porto Novo and making new grants of Egmore, Purasawalkam and Tondiarpet. But when Zulfiqar Khan requested 100,000 pagodas from the Madras Council, Nathaniel Higginson (first Mayor of Madras) sent a present, but declined to lend the sum asked. An attack on Madras is feared by the English from Zulfiqar Khan but Emperor Aurangzeb sends Zulfiqar Khan reinforcements and commands him to renew the siege of Jinji without further delay and not to waste time with the English.
When Qasim Khan, Subedar of Bijapur-Karnatak was bringing supplies to Vandavasi he was intercepted by Santa Ghorpade near Kaveripakkam. Qasim Khan took shelter behind its walls. Zulfiqar Khan, hearing of his straits, marched to his relief and escorted him safely to Vandavasi. Santa baulked of his prey, attacked and took a number of forts with their Mughal garrisons, Zulfiqar Khan at once turned back, retook the forts and entering Thanjavur took from Shahu, Vyanko's son, a large indemnity. Returning northwards, he led out his army from Vandavasi and renewed the siege of Jinji. Unable to cope with Zulfiqar Khan's military skill and the large forces at his disposal, Santa Ghorpade entered the southern province of Bijapur.