The main acropolis of Gortyna was located on Agios Ioannis hill, to the northwest of the Agora. Acropolis can be accessed from its west side driving through Ambelouzos village to the direction of Gergeri. At a spot around 1.6 kms from Gortyna parking there is a footpath (not clearly signposted and maintained) that leads to the top of the hill. Once at the top you'll be rewarded by the magnificent view to the whole area and the archaeological site itself.
The site was first inhabited in the Neolithic era and again at the end of Minoan times (1200 BC). Since then it was continuously inhabited until the Middle Byzantine period. From the first settlement only parts of walls, floors and hearths were preserved. In the 10th century BC a Geometric settlement was established fortified by a polygonal wall with towers at the corners. At the end of the 7th c. A.D., a small tripartite temple, dedicated to Athena Poliouchos was founded at the south side of the hill. From this temple some very important architectural sculptures were excavated. During the Early Byzantine period (5 - 6th century AD), a basilica was erected over the ruins of the geometric/archaic temple and, in the time of the emperor Heraclios (7th century A.D.) the last fortification with a castle in the center was built which still survives but in a very poor condition.