Copper plates dated to 758 and 768 show that, by the 8th century, an agricultural settlement known as Punnaka existed where Pune is today. The plates indicate that this region was ruled by the Rashtrakutas. The Pataleshwar rock-cut temple complex was also built during this era.

Pune was a part of Yadava Empire of Deogiri from the 9th century to 1327. It was later ruled by the Nizamshahi sultans, until it was annexed by the Mughal empire in the 17th century. In 1595, Maloji Bhosale was appointed the jahagirdar of Pune and Supe by the Mughals.

In 1625, Shahaji Bhonsle appointed Rango Bapuji Dhadphale as the administrator of Pune. He was one of the first major developers of the town, overseeing the construction of the Kasba, Somwar, Ravivar and Shaniwar Peths. Construction also began on the Lal Mahal palace, as Shahaji's son, Shivaji Bhonsle (later Chattrapati Shivaji) was to move there with his mother Jijabai. The Lal Mahal was completed in 1640. Jijabai is said to have commissioned the building of the Kasba Ganapati temple herself. The Ganapati idol consecrated at this temple is regarded as the presiding deity (gramadevata) of the city.

From 1630 to 1647, Dadoji Kondev, Shivaji's childhood mentor and teacher, oversaw development and construction in the area. As a child, Shivaji is said to have commemorated agricultural activities personally by using specially made golden ploughs. After Shivaji was crowned Chhatrapati (King) in 1674, he oversaw further development in Pune, including the construction of the Guruwar, Somwar, Ganesh and Ghorpade Peths.

Baji Rao I became Peshwa of the Maratha empire, ruled by Chattrapati Shahuji, in 1720. By 1730, the palace of Shaniwarwada had been constructed on the banks of the Mutha river, ushering in the era of Peshwa control of the city. The patronage of the Peshwas resulted in the construction of many temples and bridges in the city, including the Parvati temple and the Sadashiv, Narayan, Rasta and Nana Peths. The Peshwas fell into decline after their loss in the Third Battle of Panipat in 1761. In 1802, Pune was captured from the Peshwa by Yashwantrao Holkar in the Battle of Poona, directly precipitating the Second Anglo-Maratha War of 1803-05.

The Third Anglo-Maratha War broke out between the Marathas and the British in 1817. The Peshwas were defeated at the Battle of Khadki (then transcribed Kirkee) near Pune, and the city was seized. It was placed under the administration of the Bombay Presidency, and the British built a large military cantonment to the east of the city (now used by the Indian Army). The Pune Municipality was established in 1858. Pune was at one time the "monsoon capital" of the Bombay Presidency.

Nanasaheb Peshwa, the adopted son of the last Peshwa Bajirao II, rose against British East India Company rule in 1856, as part of the Indian Mutiny. He was helped by Rani Lakshmibai of Jhansi and Tatya Tope. After the mutiny failed, the final remnants of the Maratha empire were annexed to British India.

Pune was an important centre for the social and religious reform movements of the late 19th century. Many prominent social reformers lived here, including Mahadev Govind Ranade, Ramakrishna Gopal Bhandarkar, Gopal Krishna Gokhale, Maharshi Vitthal Ramji Shinde and Jyotirao Phule. The most important political reformer of this era was Bal Gangadhar Tilak, who dominated the Indian political scene for six decades.

Tilak was a prominent activist early in the Indian independence movement. Shivaram Rajguru and Nathuram Godse, two other important political activists, were both born near Pune.