Emporio was inhabited since the early Neolithic times (6000 BC). The region provides suitable living conditions, an ideal harbor for vessels, a cultivable plain, and a source of potable water. Around 3000 BC the settlement was destroyed by a conflagration, caused by an incursion by foreign tribes or other, unknown factors. However, it was rebuilt and during the final periods developed into a major urban center of the Aegean, covering a huge area, in the extent of 30 hectars. The focal point of the settlement was a well, protected by a series of large walls. Other walls were also discovered, perhaps belonging to a fortification, though more probably they formed a terrace, retaining the soil far from the well. The houses were one-storey, stone-built, with earthen floors and flat roofs. Specialist artisans fashioned and decorated the pottery vessels, and created tools of wood, bones and metal. Vases, in a considerable variety of shapes, were brought to light from the British School of Archeology, as well as other objects including spoons, clay figurines, spindles whorls of diverse types decorated with the same motifs as the vase, hundreds of cores, flakes and blades of obsidian and flint. All these discoveries are housed at the Archeological Museum of Chios.

The Mycenaean settlement (13th century BC) was also brought to light in the same area. The houses had large rooms and were built on the basis of a central town plan. The vases are of different shapes, decorated mainly with painted linear motifs. From the architectural evidence and the other finds, the relation between the settlements and other parts of the Aegean, such as Evia, Kea and elsewhere are surmised. About 1100 BC this settlement was destroyed by a fire and, as a result abandoned. Its demise coincides with the inception of Ionian colonization.

Temple of Athena at Emborio

Excavations on the hill of Prophet Elias revealed an archaic settlement, including a walled acropolis with Megaron and a Temple devoted to Athena. Also several houses around it and a sanctuary close to the harbor were discovered. The name of the town was probably Lefkonion. The acropolis was fortified and the rampart, approximately 800 meters long (nowadays only visible in place), enclosed an area of 25000 square meters. The entrance was at the south edge of the temple. Also in southern section of the acropolis was a sanctuary, already built in the 8th century BC. An irregularly built altar of rectangular blocks dates back to the 7th century BC. The temple was dedicated to Athena and built at the 6th century BC, while several replacement and additions were made approximately 4000 before Christ. Located in the north-east of the temple is the Megaron, overlooking the temple, the entrance of the acropolis and the main road leading down the hillside. It is an early structure going back to the 8th or the 7th century BC, and was probably the residence of the ruler. Outside the acropolis is the main settlement of over 50 houses, in which about 500 people lived. There were probably more houses that have not yet been discovered.