It is a cross-in-square church in style of architecture. The church is divided into three aisles by two rows of pillars, which culminate in three apses at the east end. The three-sided apse in the middle protrudes from the outside wall.The Knights' Headquarters, which was constructed later to the north of the cathedral, connects with it via a door in the narthex wall.
During Ottoman control, the Byzantine church was turned into a Muslim mosque. The central apse has traces of the mihrab, or prayer niche.The majority of the church's pillars and south wall are no longer in place. They were disassembled during the excavations in order to be removed. The presence of the Christian church attests to the acropolis's continuance of worship.