Fifty metres to the south of Basilica II lie the ruins of one of the few centrally planned early Christian churches found in Greece. The church dates to the 6th century and is the most imposing monument in early Christian Amphipolis. It consisted of a central hexagon with uneven sides, which, with the exception of the east side, were surrounded by an external wall built around the hexagon to create a corridor 4 metres wide.  The remains of two columns of differing size and type found inside the church point to the existence of a tribune . The floor in the nave was laid with fine white marble, while equally lavish marble revetments covered the floor of the corridor. Traces of mosaics uncovered at various points have been attributed to mosaic decoration on the walls.

The hexagon had a large apse to the east, which was semicircular on the inside and pentagonal outside. The corridor ended in two square chambers with marble floors to the east, linked to the presbytery via gates. Excavations in the southwest corner of the hexagon unearthed a rectangular chamber with a semicircular conch inscribed in a rectangle to the west; this was identified as the baptistry , on account of a water conduit penetrating the eastern wall. Leading off this room to the east was another smaller chamber. To the west of the church there was an atrium , surrounded on all four sides by galleries created by rows of two–storey colonnades with marble floors.  Three more consecutive chambers were unearthed in the north portico.