From 1614 onwards, so even before the founding of Batavia, Onrust island was used as a shipyard for maintenance to VOC vessels. During the siege of the Dutch lodge in Jayakarta in 1618-1619 Jan Pietersz Coen first proposed to build a fort on the island, but this plan was abandoned because of the lack of fresh water on the island. During the war with Bantam (Banten) (1655-1656) surveyor Johannes Listingh made a simple fortification to protect he ship yard against a surprise attack. He connected the existing buildings with a wall and added two diagonal bastions. The amount of work increased and new buildings, sawmills and even a church were added. The fortification was too small and in 1671 the design was made of a big fort with five bastions. The work started with the construction by the contractors Jan Boulan and Dionys Kelck of the stone north west bastion or Grote Battery (Big Battery) (1672-1674). The walls of the workshops were at the same time the northern curtain of the fort. In 1679 there were growing tensions between the VOC and Bantam. Governor General Rijkloff van Goens (1678-1681) ordered to close the undefended part of the fort with a palisade. In 1685 a powder house for 200.000 pound of powder was built inside the big bastion. The south west and south east bastion were built in wood (1689/1691).
After 1750 the palisade was replaced by stone walls and the bastions Touwpunt and Beeckhuys and a fence. In 1795 the Dutch demolished the fort and the main part of the buildings on Onrust. In 1800 the British burned down the remaining buildings.
Between 1980 and 1995 archaeological research was done on Onrust. Today the island is a protected monument. The historic park with the buildings of the quarantine station, foundation of the VOC fort, graveyard and museum attracts many visitors from Jakarta.