Excavations conducted in the 20th century at the Academy revealed the habitation of the area dating back to the prehistoric era. The inhabitants of that period, utilising the water and vegetation, established settlements along the riverbanks. Within the boundaries of the present-day designated archaeological site of the Academy, a prehistoric settlement was identified to the northwest of the so-called Gymnasium. In addition, at the edge of a hill in the north-western part of the site, an apsidal house with three rooms dating to the Early Helladic period (c. 2300 BCE) was uncovered. Excavator F. Stavropoulos argued that the building, with a lifespan of approximately one century, was dedicated to Akademos and named it the “House of Akademos”.

To the south of this structure, in the mid-20th century, a building from the Geometric period (8th century BCE), was discovered. The excavator himself named it the “Sacred House”, drawing an analogy to the Sacred House of Eleusis, with which it exhibited similarities. It measures 15.3 by 14.6 metres and consists of seven rooms connected with a corridor. Its walls are built with raw bricks and mud, founded on river stones. Inside the building, the excavator found pyres with burnt animal bones and fragments of vessels, a circular hearth and sacrificial pits, which led him to the conclusion that funerary banquets took place there. He attributed a religious function to the building, believing that it too was dedicated to the hero Akademos, the settler of Academia. As the Early Helladic “House of Academos” and the “Sacred House” are in immediate proximity, the excavator suggested that the memory of the prehistoric worship of Akademos persisted and that the inhabitants of the late Geometric period constructed the Sacred House to practise his worship, when they started honouring the first settlers of their region. However, this interpretation is strongly challenged today upon reevaluation of archaeological data. As numerous burial vessels with child cremations were found around the house, some researchers suggest that while the site was indeed sacred, it was dedicated to some other, abstract ancestral cult. Others believe that the building was originally the home of a prominent figure, which was later destroyed and abandoned. Some time after, a cult with purification rituals related to child burials began to be practised there. According to recent research, these child burials had been transferred from the surrounding area near the building.

The Sacred House, like the apsidal building, was roofed for protection from weathering; however, the terrain configuration in the area results in recurrent flooding. In 1961, due to a major flood, the brick walls of the building were destroyed and in 2001, following a very heavy rainfall, the site was covered by five metres of water. Today the Sacred House is covered up and only its plan is indicated on the ground layer.