The Hiera Oikia (Temple of Zeus) with the oracular oak-tree had a rectangular structure, measuring 20.80 x 19.20 m and at least four building phases. The original nucleus consisted of a small temple with a pronaos and cella dating to the first half of the 4th c. BC.

At the beginning of the 3rd c. BC, in the reign of King Pyrrhus (297-272 BC), the ashlar precinct was replaced by a larger one with Ionic colonnades on three sides of the court and an entrance in the front; on the east side, where the oak-tree stood, there was no colonnade. The interior layout was characteristic, with a court and the colonnades in the form of a Π enclosing the lofty Oak-tree where the God lived. In these colonnades Pyrrhus hung the Roman shields he captured after his victory at Heraclea in Italy (280BC) and the votive inscription preserved on a part of a shield, now in the National Museum of Athens.

In 219 BC the Aetolians made a sudden attack on Dodona and Dion, the holy city of the Macedonians, and looted the two Sanctuaries. According to the 2nd c. BC historian Polybius, the Aetolians burnt down the Sanctuary Dodona; the Hiera Oikia, however, they did not burn, but demolished. The different treatment of the Hiera Oikia can be explained if we remember that it was here that the Oak-tree stood which was the god's abode, and that burning down would have destroyed the tree; this would have constituted a great sacrilege and stirred up popular indignation throughout Greece. We have therefore good reason to suppose that this building, which shows no traces of burning, was the Hiera Oikia mentioned by Polybius.

In the autumn of the following year (218 BC) the Macedonians and Epirotes, to avenge the destruction of Dion and Dodona, attacked Thermos in Aetolia and burned and plundered it. With the booty they captured, which was considerable, they rebuilt the destroyed Sanctuaries at Dion and Dodona. The Hiera Oikia was now refurbished on a more monumental scale. A larger one with an Ionic tetrastyle pronaos, cella and adytum, having three Ionic columns in the front, took the place of the small temple. On the side of the Oak-tree a deep hole and hewn stones were found, probably from an altar. The exterior east wall has suffered subsidence in this place, due to the hole left by the uprooted tree.

The excavations have not uncovered any evidence for the fate of the Temple when the Romans (167 BC) burnt down the Sanctuary and other buildings. In the 2nd c. AD, Pausanias described the Sanctuary with the Oak-tree as "worth-seeing", and the Naia were still being celebrated in 240 AD. The final end of the Hiera Oikia came at the end of the 4th c. AD, when the oracular Oak-tree was cut down and a huge hole excavated in order to uproot it or else in search of treasure.