The Early Bronze Age or Early Helladic Period (3000-2000 BC) represents something of a gap in the history of the Athenian Agora area. The finds from this period are scarce, mostly potsherds. On the contrary, the area is greatly developed in the second millennium, during the Middle (2000-1600) and the Late (1600-1100) Helladic Period. 

During the Middle Helladic Period, human presence is traced in the area surrounding five wells situated on the NW corner of the Acropolis, which are dispersed among the more numerous ones from the Neolithic Period. Several shards from of the Gray Minyan wares have been discovered scattered in the Agora area (these are ashen pots with a soapy surface, crafted on a potter's wheel), as well as from the Lustreless type, decorated with simple geometrical patterns. There are no traces of buildings or burials, however. 

The Agora area is particularly prosperous during the Late Helladic Period (1600-1100). This is a time during which the Mycanean civilization is burgeoning in Athens. During this period the Athenian Agora functions as a burial ground, but also as a residential area. The city's administrative centre is located on the Acropolis, while the settlement expands mainly around the Acropolis, in a zone south of the rocky projection, an area where natural springs provided the necessary water supply. According to mythological accounts, the end of this period (1200-1100 BC) is marked by the synoecism of Attica’s communities (kōmai) by Theseus, and this follows an earlier (1500 BC) and less extensive synoecism of fifteen settlements by Cecrops. Theseus's unification is in effect a coalition of scattered settlements under the aegis and power of a king, residing on the Acropolis palace. 

Very little is known about Late-Helladic Ι in Athens, the first phase of the Mycenaean civilization, and that mostly through potsherds. Several traces of the next phase (Late-Helladic ΙΙ), which corresponds to the 15th cent BC (1500-1400) remain, however, on the Acropolis. The heyday of Mycenaean Athens is identified with the third phase of the Late-Helladic Period, especially in its early years (approx. 1410-1380 BC). The population spreads to the entire south part of the city. It is, however, possible that a new settlement had been formed on the north of the Acropolis, which used the Athenian Agora as a burial ground. Two more important cemeteries are located on the Areios Pagos, featuring splendidly rich burrials, and at the foot of the Hill of the Nymphs. 

In the Athenian Agora area there is a large number of burials from the LH ΙΙ and LH ΙΙΙ Α Periods (16th -14th cent.), while very few of these are dated to the LH ΙΙΙ B and C (13th -12th cent.). Forty-one tombs have been excavated in total in the Mycenaean cemetery of this area, 21 out of which were chambered tombs accessed via a different way. The pit graves are also relatively widespread (12 examples). The more luxurious of the chambered tombs are the ones excavated on the north slope of the Areios Pagos, outside the main cemetery. The chambered tombs were small in size, mainly on account of the hardness of the rock out of which they had to be carved. In some cases there are multiple burials: tomb VII is noteworthy, in that it contained 25 burials and a number of lavish funeral gifts, in an area measuring just 5.5 m².Most burials are of the same type: the deceased was placed close to the entrance of the chamber, in an expanded or a contracted position. In the pit graves there occur other types of burials (inside small wooden coffins, cenotaphs, children’s graves etc.). The adults buried in pits obviously belonged to the lower social strata, as they were accompanied by precious few burial gifts. 

Apart from the graves, in the Agora area there are also numerous wells containing Mycenaean pottery, while traces of streets also exist on the NW corner of the Agora, in the Tholos area on the west, and in the South Square area. These streets are generally dated to the Neolithic or the Early Helladic Period, but there are indications of their being used during the Mycenaean Period as well.

The glorious history of the Late Mycenaean city comes to a violent end in the beginning of the 12th cent. BC. Although the size of the city's area does not change, the habitation density now diminishes greatly, with widespread residences. The centralised economy of the Mycenaean palaces collapses and isolation, cessation of commercial exchanges and a general deterioration of material culture ensue. The wide dispersal of the cemeteries, with clusters of a small number of graves, testifies to the return of an agrarian form of land usage, dominated by farmhouses.