The museum is located within the archaeological site, and houses exhibits of ancient Eleftherna and the Necropolis of Orthi Petra. The permanent collection presents objects of art and everyday life from prehistoric, geometric, archaic, classical, Hellenistic, Roman and Byzantine times.
The museum has three galleries. The first one presents imported objects from areas outside Crete that highlight aspects of public and private life in the city. The second gallery is about religion and worship in Eleftherna from the early Iron Age to the Byzantine era. The third gallery displays impressive grave offerings and highlights funerary practices from the necropolis of Orthi Petra.