The fortified city of ancient Alipheira stretches across a terraced hilltop over an area of 800 x 65 metres. The city's acropolis, which had its own fortification wall, occupies the highest terrace in the east. East of the acropolis, at a lower level, is the temple of Athena; the temple of Asklepios is located further west. Excavations also revealed two rectangular enclosures, which belonged to private or public buildings.


Only the hill's more easily accessible and, therefore, vulnerable parts (north, east, and east half of the south side) were fortified. Gates were probably located on the east, which was naturally accessible, and northwest, near the Asklepieion. The acropolis proper had its own trapezoidal enclosure of polygonal masonry with three towers and a trapezoidal entrance passage-way; it dates from the fifth century BC.


The goddess Athena was allegedly born and raised in Alipheira, hence the importance of her sanctuary and the presence of the altar of Zeus Lecheatos mentioned by Pausanias. The sanctuary lies east of the acropolis on a terrace with stepped access. It comprises a Doric peripteral temple of the Late Archaic period, a large altar, and the inscribed pedestal of a colossal statue of Athena. The προάστιον της άκρας, mentioned by Polybius (IV, 78, 11) in his description of the city's siege by Philip V, was probably located on the flat fortified crag east of this plateau.


The Asklepieion, Alipheira's second most important sanctuary, also mentioned by Pausanias, was discovered in the fortified city's western part. It comprises a temple (distyle in antis), an altar, and part of a building, which probably served the needs of the priests or the devotees.


The lower city, which probably stretched north and east of the fortified city, may have been protected by an outer wall, or proteichisma. The Tritonis spring, which relates to the myth of Athena's birth near the Triton river, was identified here. A cemetery with monumental tombs of the Hellenistic period is located at the east end of this area.