Khanderi, along with its sister fort Underi (Jaidurg) formed the major fortification along the Maharashtra coast, the former falling under Shivaji Maharaj's control and the latter under his opponents, the Siddis.

In 1679, Khanderi was occupied by the forces of Shivaji under the leadership of Maynak Bhandari, who oversaw the building of the fortifying walls.

[4] Subsequently, Khanderi fort was built during the reign of the Maratha Emperor Shivaji Maharaj in 1679 CE[5] to keep a check on the Siddis at Murud-Janjira fort and was the site of many battles between Shivaji's forces and the navy of Siddi.

[6] In 1813 Manaji Angre handed over the fort to Peshve in return of the support given against Baburao.

[7] The fort was subsequently ceded in 1818 to the forces of the British East India company at Bombay as part of the Peshwa territory.