The Museum is housed in the church of the Venetian Monastery of St Francis.

During the course of its centuries-long life, the building has been used for many different purposes and modified accordingly. It was converted into the Mosque of Yusuf Pasha and later turned into the Idaeon Antron Cinema and a military depot.

It opened as an Archaeological Museum in 1963. Its interior modification was carried out in the period 1977-1981.

In 2000, three small storerooms on the north side of the Museum, adjoining the church of St Francis, were modified to house the permanent exhibition of the Konstantinos, Marika and Kyriakos Mitsotakis Collection, which was donated to the Archaeological Museum of Chania.