Between 1631 and 1875 the fort was won and lost nine times by the nations contesting control of Mombasa. It was declared a historical monument in 1958. Today it houses a museum.

The fort was designed by a Milanese architect, Giovanni Battista Cairati, who was the Chief Architect for Portuguese possessions in the East. It was the first European-style fort constructed outside of Europe designed to resist cannon fire. Today, it is one of the finest examples of 16th century Portuguese military architecture, which has been influenced and changed by both the Omani Arabs and the British. The fort quickly became a vital possession for anyone with the intention of controlling Mombasa Island or the surrounding areas of trade. When the British colonised Kenya, they used it as a prison, until 1958, when they converted it into a historical monument. James Kirkman was then assigned to excavate the monument, which he did (withQQa large use of external historical documents) from 1958 to 1971.