In January 1599, the Portuguese erected a triquetra (a wooden stockade) on the site. In 1603 the Portuguese were forced to withdraw from the area by the Kandyan forces. In 1626, under the supervision of the Portuguese Governor, Constantino de Sá de Noronha, the fort was upgraded and strengthened, the rectangular fortification was known as the Forte Santa Fe or the Cidadela (Citadel) of Forte Cruz, it had four bastions on each corner, named Saõ Iago, Saõ Boa Ventura, Saõ Jorge and Saõ Pedro. The fort was not a major structure, and its status as a fort is questionable given that it consists mainly of earth ramparts. It did, however, play an important strategic role against the Kandyan kingdom as the main marshalling point for Portuguese forces in their ongoing fight against the Kingdom of Kandy.
It was recorded that approximately 400 Portuguese soldiers were garrisoned in the area. In the 1630s, the fort fell to Kandyan forces as the result of ongoing rebellion against the Portuguese invasion of the Kingdom of Kandy. The Portuguese, however, re-captured it. Following the defeat of the Portuguese in 1658, the area was re-occupied by the forces of the Kingdom of Kandy.
The Menikkadawara fort lost its strategic role once the Dutch secured control of Ceylon. Today the only remains of the fort that are visible are the earthen ramparts, which are overgrown with grass and weeds. The only other indication of the former fort is a sign erected on the site by the Department of Archaeology Department.