The most important buildings of the site are:

The Palace. The largest part of the ruins visible today belongs to the New Palace period; of the first palace only a section is preserved, to the NW of the building, while a small oblique structure in the north court dates to the Post-palatial period. Access to the palace today is through the west paved court, which is crossed by slightly raised paths, the so-called "processional ways". Every side of the complex had an entrance, but the main ones were those in the north and south wings.

The palace is arranged around the central court, which had porticos on the north and east sides, and an altar at the centre.

The largest and most important part of the palace is the two-storeyed west wing with cult and official appartments, and extensive magazines. Impressive is the Loggia, a raised hall opening to the court, and the rooms to the west, all related with cult practice, the "pillar crypt" with an antechamber, also of religious character, and between these two, the grand staircase leading to the upper floor. Another broad flight of steps, possibly used as a theatral area, is located to the SW of the central court, beside the famous "kernos" of Malia.

The south wing, also two-storeyed, included habitation rooms and guests' rooms, a small shrine, and the monumental paved south entrance to the palace that led directly to the central court.

The SW corner of the of the palatial complex is occupied by eight circular structures used for the storage of grain (silos).

The east wing is almost completely occupied by magazines of liquids, with low platforms on which stood pithoi (large storage vessels), and a system of channels and receptacles to collect liquids.

Behind the north stoa of the central court is the "hypostyle hall" and its antechamber. Above these rooms, on the upper storey, there was a hall of equal size, interpreted as a ceremonial banquet hall. To the west of these rooms, a stone paved corridor connects the central court with the north court, which is surrounded by workshops and storerooms, and with the NW court, also called "court of the dungeon". To the west of this lie the official rooms of the palace: at the centre, the reception hall with the typical Minoan polythyra, and behind this, the sunken lustral basin.

The palace is surrounded by the town, one of the most important Minoan towns in Crete. To the north of the west court is the agora and the curious "hypostyle crypt", which has been interpreted as a kind of council chamber, connected with the prytaneia of historic times.

The most important of the excavated sectors of the town and isolated houses are sector Z, houses E, Da, and Db; very important is sector M, dated to the First Palace period, which covers an area of c. 3,000 sq.m. and is actually the most important settlement of this period in Crete. The unusually extensive buildings of this neighbourhood included religious, official, and storage rooms, and workshops, and it seems that in general, it had functions similar to those of the palace.

The cemetery of the First Palace period is located to the NE of the palace, near the north coast. The most important of the graves found is the large burial complex called Chryssolakkos, which yielded the famous gold bee pendant.