The continuation of human activity during the Classical and Hellenistic periods is currently documented by few, but remarkable findings. During a rescue excavation at the eastern end of Daedalou Street, abundant pottery of Classical and early Hellenistic times and four burials were found, including one from the 3rd century BC. On the same layer and north of the burials the foundation of the wall was established, with architectural elements of the Classical period in second use.

In the area west of the Archaeological Museum, where the ancient settlement extended, sherds of Attic vases have occasionally been found, either individually or in large deposits. Between Idomenos – Daedalou – Merampelou streets lies the area of the ceramic workshops producing amphorae for the export of oil and wine. In the square opposite the Hotel Hesperia between Idomeneos – Merampelou – Aretousas streets and a little further north on Idomeneos Street, large deposits of pottery were found, including, Attic red-figure vases. At 22 Milatou Street, at a depth of 4 m, a thick layer of broken amphorae, chimneys, traces of a kiln and several amphorae were found, indicating the existence of a production workshop. Imprinted wine amphora handles from the research carried out during the expansion of the Archaeological Museum preserve inscriptions with the names of workshops and potters from Rhodes, Thassos and Kos dating back to 290-280 BC, proving that the wine trade flourished, especially after the middle of the 2nd century BC. The research also uncovered meagre building remains of the Hellenistic period, typical pottery of the West Slope ware and two relief busts on vase handles.  A handle of a wine amphora was also found in Stratigou Marineli street in the western part of the city near the coastal front. Fragments of vessels of everyday use of the Hellenistic period have been found in recent years in various excavations in the historic centre, such as in Stratigou Marinelli str, in Papagiamali str, in Koronaiou str, in Tsouderson & Soumerlis str, in the area of Vigla  and in the foundations of the Vikelaia Library. On the coastal front, at the church of St Peter of the Dominicans, Hellenistic pottery was found on the natural ground in excavation trenches.

In monetary terms, the Hellenistic period is represented by 24 coins from Knossos, Gortyn, Lyttos, Axos, Aptera, Raukos and Kydonia, covering a period from the 3rd to the 1st century BC and testifying to the commercial relations of Herakleion with other Cretan cities.

The finds south of the course of the fortification are exclusively of burial character. A tombstone with a reception scene, dated to the third quarter of the 4th century BC, was found in 1955 during the excavation of the foundations of the Astoria Hotel in Eleftherias Square. On the same plot in 1966, a 2.00 m wide section of a fortification made of dressed stone blocks was found in the extension of the Zouraris plot. In 1969, a marble female head of the same period was found on a plot near the previous one. The Attic-style sculptures were attributed to local craftsmen who were trained in workshops in Athens. In the same year, a burial with figurines of the Hellenistic period and other rich grave goods was found at 38 Evans st. More recently, in the same area, at the junction of 1866 and Giannitson str, another Hellenistic burial was found, with unguentaria and gold lamellae. The dispersion of the burial finds documents that the Hellenistic southern necropolis of Herakleion occupied a zone at least 200 m wide south of Daidalou Street and extended at least 300 m from Eleftherias Square to Evans str, perhaps even further west. The boundary between the town and the necropolis seems to coincide with the course of the fortification of dressed stones found in Daidalou str and Eleftherias Square.