Until 1657, Shivaji maintained peaceful relations with the Mughal Empire. Shivaji offered his assistance to Aurangzeb who then, was the Mughal viceroy of the Deccan and son of the Mughal emperor, in conquering Bijapur in return for formal recognition of his right to the Bijapuri forts and villages under his possession. Dissatisfied with the Mughal response, and receiving a better offer from Bijapur, he launched a raid into the Mughal Deccan. Shivaji's confrontations with the Mughals began in March 1657, when two of Shivaji's officers raided the Mughal territory near Ahmednagar. This was followed by raids in Junnar, with Shivaji carrying off 300,000 hun in cash and 200 horses. Aurangzeb responded to the raids by sending Nasiri Khan, who defeated the forces of Shivaji at Ahmednagar. However, Aurangzeb's countermeasures against Shivaji were interrupted by the rainy season and his battle of succession with his brothers for the Mughal throne following the illness of the emperor Shah Jahan.

Upon the request of Badi Begum of Bijapur, Aurangzeb, now the Mughal emperor, sent his maternal uncle Shaista Khan, with an army numbering over 150,000 along with a powerful artillery division in January 1660 to attack Shivaji in conjunction with Bijapur's army led by Siddi Jauhar. Shaista Khan, with his better–equipped and –provisioned army of 80,000 seized Pune. He also took the nearby fort of Chakan, besieging it for a month and a half before breaching the walls. Shaista Khan pressed his advantage of having a larger, better provisioned and heavily armed Mughal army and made inroads into some of the Maratha territory, seizing the city of Pune and establishing his residence at Shivaji's palace of Lal Mahal.

In April 1663, Shivaji launched a surprise attack on Shaista Khan in Pune, along with a small group of men. After gaining access to Khan's compound, the raiders were able to kill some of his wives; Shaista Khan escaped, losing a finger in the melee. The Khan took refuge with the Mughal forces outside of Pune, and Aurangzeb punished him for this embarrassment with a transfer to Bengal.

In retaliation for Shaista Khan's attacks, and to replenish his now-depleted treasury, in 1664 Shivaji sacked the port city of Surat, a wealthy Mughal trading centre.