The Archaeological Museum of Chania is subject to the Ephorate of Antiquities of Chania. The Museum has been housed in the church of the Venetian Monastery of St Francis since 1963.  The exhibits illustrate the cultural history and character of the area through the ages, from the Neolithic period to the Roman era. The exhibition hall is divided widthwise into two major sections. The east wing contains finds of the Late Neolithic period and the Bronze Age (Minoan era), while the west wing presents antiquities dated to the Iron Age (Historic era). The finds are presented in excavation groups and thematic units. The collections comprise Minoan finds from the city of Chania, prehistoric finds from caves, Minoan finds from various parts of the Prefecture, finds from tombs of the Geometric period, finds of the Historic era from Chania and various other towns and cities in the Prefecture, coins, prehistoric and historic jewellery, sculptures, inscriptions, stelai and mosaics.

The fascinating Konstantinos, Marika and Kyriakos Mitsotakis Collection was donated to the Archaeological Museum of Chania in 2000. It is housed in three small rooms on the north side of the Museum, adjoining the church of St Francis. The objects on display comprise one-third of the Collection and are presented in chronological order (late 4^th millennium BC – 3^rd c. AD). They include examples of Minoan pottery, clay models, stone-carving, seal-carving, jewellery and varia (various objects from different areas).

The Museum has its own conservation laboratories for pottery, metal artefacts, coins, frescoes and mosaics, as well as a chemical laboratory. There is also a museum shop run by the Archaeological Receipts Fund in the converted belfry next to the main entrance. The aim of the Museum is to promote local cultural history in the best possible way, in order to make the Museum a major attraction drawing large numbers of visitors. Means of achieving this include temporary exhibitions, educational programmes and various events held in the Museum.