Along with many other cities in Crete, Palekastro was burnt at the end of the Late Minoan IB period, but grew again in the Postpalatial period, (Late Minoan IIB) until it became the largest town in eastern Crete. The location of the town was important as it was on the east coast, with a large plain behind it and a harbour that was sheltered by an outcrop of rock called Kastri hill.

Much of the earliest excavations at Palekastro have since been covered over again with earth and the site suffered damage during the war and also from a bulldozer. The parts which can be seen include houses and streets, with the long main street running east-west, though no palace/temple has yet been found.

Castleden argues that the absence of a palace/temple meant that the craft workers may have been able to carry out their trade geographically separated from the palace/temple, although the possibility cannot be excluded that their work was directed by the priests at Zakros, further down the east coast.

To the south of the site a Peak Sanctuary was excavated by the British on the summit of Petsophas, 225 metres high. It proved to be one of the richest and most important Middle Minoan Peak Sanctuaries and was certainly still in use in Late Minoan I, when a small cult building was erected. A very large number of small clay figurines of men and women, representing the people making the dedicatory offerings were found, which provided a lot of information about the dress and hairstyles of the period. Votive models of human limbs and stone offering tables with Linear A inscriptions were also found.

The finds from Palekastro are exhibited in the Museum of Sitia.