The settlement of Dodona was on the acropolis, just to the north of the temenos and 25m above the sanctuary. It offered space for around one thousand inhabitants. It may be that the officials of the sanctuary of Zeus at Dodona dwelt there; it would also have offered refuge for the population of Dodona during times of danger.

The area has not been excavated, so very little is known about the site itself, although the remains of several buildings have been found there, as well as a subterranean water cistern.

In the fourth century BCE, when the first temples to Zeus were built in the sanctuary, a wall was built around the acropolis, with rectangular towers on the north, west and south sides. The wall had three gates: one to the east that led down to the Ioannina plain; one to the south, protected by one tower; and the largest to the south-west, protected by two towers, which led down into the sanctuary and theatre.