In the Prehistoric period, Kronos, Rhea, Gaia, Themis, Eileithyia, Hercules Idaios and other deities were venerated at the foot of the Kronios hill, at the very site occupied by the Altis in later times. Here excavations revealed a primitive sanctuary and possibly a settlement of the Early Helladic III period (2300-2000 BC); the site was continuously occupied until the Late Helladic III period (1600-1100 BC).

Several prehistoric buildings in the area of the Heraion have been investigated and back-filled. Building III, the only building still visible, is situated south-east of the Heraion, below the Archaic and Classical levels of the temple. It is an apsidal structure oriented north-south. The surviving lower course of the walls is of irregular stone, while the upper part of the walls was probably of perishable materials. Pottery finds date the building to the end of the Early Helladic III period (2150-2000 BC) and indicate contacts with the Cetina culture in the Dalmatian coast. These apsidal buildings, together with the Prehistoric tumulus inside the Pelopion, are the oldest surviving structures in the sanctuary.

The monument is closed to the public.