In that historical period, traces have been discovered of a palace that included a megaron, a courtyard used for audiences and meetings. It cannot be confirmed with certainty whether a temple dedicated to Athena already existed at that time. The term megaron, of Greek origin but possibly with Semitic influence, referred to the "great hall" that was usually located in the palaces of the Mycenaean civilization in Greece and Anatolia. It was usually located at one end of the central courtyard, just in front of the altar, and consisted of three parts: an open portico with two columns in antis, a vestibule or anteroom, and the main hall known as naos.

Towards the end of the Helladic IIIB period, covering the years 1300-1200 B.C., an imposing wall was built around the acropolis, which reached a thickness of up to 6 meters. In addition, a fountain located on the northern slope of the acropolis also dates back to the Mycenaean period, as pottery finds there indicate that it was built at the end of the 13th century BC.

There is debate as to whether the entry in the Iliad's catalog of ships, which describes a temple in relation to the Athenian contingent, reflects a Mycenaean period or a later period.