In the greater area, there are many prehistoric settlements, which shows the existence of a community, which continued to exist in the Neolithic era, where people were occupied not with hunting but with agriculture and cattle breeding until the Copper era.

There are references to the area of Chalkidiki during the period of the Greek mythological times. According to the poet Hesiodus about the birth of the man and the gods, the first man was popped out of the earth in the area of Kassandra in Chalkidiki, which was then called Pallini or Flegres by the name of a giant.

In the area of Pallini the famous gigantomachy took place. It was between the sons of Uranus and Gea and the Olympian Gods. The fight was still in balance, until Zeus asked help from the immortal sons of Hercules and Dionysus and finally the Olympian Gods won. 

During the period of the gigantomachy, the goddess Athena threw the peninsula of Kassandra at the giant Engelados; then the giant Athos threw the third peninsula of Chalkidiki at the Olympians. The gigantomachy was an inspirational subject for many artists and poets of that time. There are findings in the Archaeological Museum of Athens that verify this inspiration.

With the appearance of copper, the first inhabitants of that area are considered to be the primitive race of Proellines Pelasgi, who were gathered in the peninsula of Athos. Pelasgi used to live near Thrace on the east side of river Nestos that is why the ancient Greeks used to call them Thracians. 

During the period of Trojan War, on the west side of Chalkidiki, Trojans settled there, having Enia as their leader. He was the one who built the homonymous city.

In the peninsula of Kassandra, after the end of Trojan War, the Pellines of Achaia found refuge there and renamed the area to Pallini. The colonization of the peninsula started in the beginning of 8th century with settlers from the area of South Greece and mainly from Halkida, Eretria and Evia. The first colonies of the area were "Agea", "Halkis", "Mendi" and "Afytis". The colonization continued by the Corinthians who founded Potidea, by the inhabitants of Andros who founded the birth place of Aristotle, Stagyra and by Athenians who, along with the inhabitants of Halkida, founded the famous city of Olynthos.

Most of the settlers were coming from Halkida and had settled in the area of Sythonia and in the center of Chalkidiki. The name Chalkidiki comes from the inhabitants of Halkida. During the ancient times, it used to be called "Chalkidiki, the one in Thrace". Around the beginning of 7th century, Vottees came to this area, chased away from Macedonia, and settled between Olynthos and N. Kallikratia. They renamed this area to Vottiki.

The rich timber, the fertile land, the rich deposits of gold, silver and lead and the trade between the cities of south Greece and Hellespont encouraged many cities to build colonies. Around the beginning of 6th century, the above cities controlled the trade in the area of Macedonia while the commercial transactions reached South Italy.

During the period of the Hellenistic and Classical times, the area of Chalkidiki counted more than 40 cities and hundreds of settlements. According to the archaeologists, Chalkidiki is characterized as "Attica" of north Greece. Findings from the above cities are in the Archaeological Museum of Thessaloniki. Herodotus mentions Chalkidiki in the "Persian Wars" (492-479 BC) and particularly the cape of Athos, in which the naval fleet of Mardonius, with 300 ships and 30,000 men, was destroyed.