The exact date that the building was constructed is unknown although it was mentioned in writing as standing during the great earthquake of 1595 and being the largest in the city. It served as a Venetian church inhabited by Franciscan monks, and became an important monument of the city. During the period of the Ottoman occupation, the building was used as a mosque and named after Yussuf Pasha, the conqueror of Chania. At the turn of the 20th century it became the “Idaion Andron” Cinema and after World War II it served as a storehouse for military equipment, until it was converted into the museum in 1962. The archaeological collection of Chania itself was formerly housed in various public buildings such as the Residency, the Boys’ High School, and the Hassan Mosque. In May 2008, the Crete Gazette announced that a new museum building is due to be constructed in the Chatzidakis Camp in the historical Chalepa area of Chania overlooking the sea. The modern building, designed by Theofanis Bobotis, who also designed the Patras Museum, will cover 6,500 square meters, including 1,800 square meters for exhibition halls, 140 square meters for the gallery and a 140-seat amphitheatre. The new archaeological museum of Chania will also include interior and open-air exhibition areas, skywalks, a shop, a cafeteria and other visiting rooms.
The museum contains a substantial collection of Minoan and Roman artifacts excavated from around the city of Chania and the surrounding regional unit, including pieces from the ancient cities of Kydonia, Idramia, Aptera, Polyrinia, Kissamos, Elyros, Irtakina, Syia and Lissos, and also from Axos and Lappa in Rethymno regional unit. The museum contains a wide range of coins, jewellery, vases, sculpture, clay tablets with inscriptions, stelae and mosaics. The collection includes a clay sealing from Kasteli, with a representation of a Minoan city and its patron deity dated to the second half of the 15th century BC. There is a clay pyxis with a representation of a kithara player excavated from a chamber tomb in the area of Koiliaris in Kalyves-Aptera dated to 1300–1200 BC. There is also a clay tablet inscribed with Linear A script from Kasteli, dated to 1450 BC and small clay tablets with texts in Linear B script dated to 1300. The museum has a Roman floor mosaic, depicting Dionysos and Ariadne. The Archaeological Museum of Chania also has an ancient Cycladic style vessel from Episkopi, Kissamos and a number of busts including one of Roman emperor Hadrian, found at the Dictynaion sanctuary in 1913 and a late Minoan sarcophagus from the necropolis of Armeni, dated to 1400–1200 BC. There is also a spherical flask, noted for its unusual ceramic type, dated to the Late Minoan III period.