The main building in the complex was constructed in early 1890s to serve as the District Collector's Office for the Imperial British East Africa Company.

[1] When Kenya became independent in 1963, the British-appointed District Officer was replaced by Sheikh Azzan Bin Rashid, who had previously served as the Liwali of the Sultan of Zanzibar.

In July 2012 the District Commissioner moved to new offices and the building was handed over to the National Museums of Kenya.

During the colonial period four decorative cannons were mounted around the main house: three made from iron and one from bronze.

These are: the Vasco da Gama Pillar, the Portuguese Chapel, the House of Columns and the Malindi Heritage Complex Museum.