The palace at Mallia is situated on the edge of a plain of the same name at a small distance from the sea. Its position both facilitated contact with the fertile inland and sea trade. The necropolis of Chryssolakkos and the peak sanctuary of Prophitis Ilias are nearby.

The palatial complex was surrounded by the important buildings of the city of Mallia, and seems to have followed a similar historical course to those of other Minoan palaces. The palace was constructed of local building materials such as sandstone and conglomerates. Excavations have confirmed the existence of two stories. The northern entrance, from the side of the sea, was the main entrance. The so-called oblique building, an example of the Mycenaean rule, is located near this entrance. The main point of reference of the palace was the central court, which had a central altar and stoas on both sides. There were also smaller courts on the northern section, while it is believed that the northwestern wing had internal gardens. On the west wing were all the private quarters, the rooms for public ceremonies and a series of cult rooms. The 'loggia', a raised room with a pillar which communicated directly with the central court is thought to have been a throne room, like the one at Knossos. At the back of the room was a treasury.

The adjoining buildings were probably ivory workshops and metal works, and behind the workshops was a lustral basin. South of the 'loggia', there was a staircase, presumably leading to the Piano Nobile of the upper floors. Another big room with a pillar crypt is was an assembly area. These apartments are separated from the magazines of the west wing by a long walkway. In the south area of the west wing, a very wide staircase constitutes a theatral area in miniature, where a stable stone kernos was recovered. A separate apartment, south of the theatre, with benches and cult objects has been defined as a shrine.
In the north wing there were also public areas which were important for the functioning of the palace, e.g. a large pillar room with columns and a shrine. Around the northern court were the magazines, the workshops and an oil-press. The eastern side was occupied by magazines with low terraces for placing pithoi and culverts. On the southwest end of the palace were two rows of kouloures which were probably used as granaries. The south wing was occupied mainly by workshops.
Certain masterpieces of Minoan art have been discovered at Mallia, most notably two small swords with gold inlay hilts, a stone triton with a relief representation, and ritual weapons.