This mosque, formerly a church, has seven building phases:

Phase 1 is the original version of the building and has a nearly square plan and three naves. The cross-plan naos is wider than the lateral naves. A semicircular apse was added to the eastern end of the naos. The narthex is at the west end of the building. Additional supporting piers were erected, and the naos and the lateral naves were covered with domes and vaults when the church was brought closer to the “Enclosed Greek Cross” plan in the Third Phase, which is probably dated to the eighth century. A cross-plan entrance was added to the west of the church in Phase 4, which dates to the twelfth century. A major restructuring project took place in Phase 5 during the first decade of the thirteenth century, probably after the building suffered severe damage from an earthquake. The new arrangement transformed the church into a basilica with a gallery and a gable roof. A second small apse was also added to the first.

The north and south arms of the cross-plan naos were separated by load-bearing piers, creating new lateral naves. Thus, the central structure was replaced with a basilica plan structure with five naves. The minor renovations of Phase 6 and its conversion into a mosque in Phase 7 are dated to the early sixteenth century.

The building was heavily damaged during a fire in Kaleiçi, after which it was abandoned and filled with waste. Excavations in the 1990s revealed its plan and other nearby ancient remains such as a stoa and monopteros. A restoration project in 2022 saw the repair of its collapsed walls, the strengthening of weak walls, and the rebuilding of its minaret before it was opened to worship and visitation.