Human presence at Malia during the Neolithic period (6000-3000 B.C.) is attested only by potsherds, but habitation was continuous from the middle of the 3rd millennium B.C. until the end of Prehistory.

The houses of a Pre- palatial settlement (2500-2000 B.C.) have been found under the palace, and graves of the same period are located near the sea. The first palace was built in around 2000-1900 B.C. The already existing significant settlement, parts of which are preserved around the palace, was then converted into a palatial centre-city. The palace was destroyed in around 1700 B.C. and rebuilt in 1650 B.C. at the same site, following the plan of the older palace, while a few changes were made 50 years later. The new palace was destroyed in c. 1450 B.C., along with the other Minoan palatial centres. The site was reoccupied for a short period in the 14th-13th century B.C. Remains of a Roman settlement cover an extensive area at a site called "Marmara", where a basilica of the 6th century is also preserved.

The English admiral Th. Spratt, who travelled to Crete in the middle of the 19th century, reports the finding of gold sheets at the site ""Helleniko Livadi" ". In 1915, Iosif Hatzidakis started a probe excavation on the hill called ""Azymo"" and brought to light the southern half of the west wing of the palace, as well as the tombs by the sea, but he stopped the research. Finally, the French School of Archaeology at Athens resumed the excavations, which are being continued until presently with intervals, at the palace, the sectors of the town and the cemeteries on the coast. The results have been published in the series Etudes Cretoises since 1928, and in the works of H. Van Effenterre and O. Pelon. The finds are exhibited in the Museum of Heraklion, and some of them in the Museum of Agios Nikolaos.