Major rebuilding and construction was done by Peisistratos, then later Kimon, and finally Pericles. Further modifications were made throughout the centuries and the Sanctuary was extended in the 4th century BC. A new gate was added to the sanctuary during the Pax Romana.

In 170 AD, the temple was sacked by the Sarmatians but rebuilt by Marcus Aurelius. Aurelius was then allowed to become the only lay-person to ever enter the anaktoron. As Christianity gained in popularity in the 4th and 5th centuries, Eleusis' prestige began to fade. Julian was the last emperor to be initiated into the Eleusinian Mysteries. Emperor Valentinian permitted the the continuance of the Mysteries, but Emperor Theodosius' anti-pagan laws and the sack of temple in 395 AD proved to be a death-blow to the cult. By the Byzantine era, the town had been abandoned, not to be reoccupied for over a thousand years.