The first building on this site was a Roman bath, followed by a sixth-century (the dating was based on precise coin finds in stratigraphic excavation) hall church with an apse laying up against the Aqueduct of Valens.

A third church, which reused the sanctuary and the apse (later destroyed by the Ottomans) of the second one, can be dated to the end of the twelfth century, during the late Comnenian period.

[3] In 1746, Hacı Beşir Ağa (d. 1747), the Kizlar Ağası of the Topkapı Palace,[4] built a mihrab, minbar and mahfil, completing the conversion of the building into a mosque.

[7] The building has a central Greek Cross plan with deep barrel vaults over the arms, and is surmounted by a dome with 16 ribs.

Two small chapels named prothesis and diakonikon, typical of the Byzantine churches of the middle and late period have survived.

The interior decoration of the church, consisting of beautiful colored marble panels and moldings, and of elaborated icon frames, is largely extant.

The building possesses two features which both represent a unicum in Istanbul: a mosaic, one meter square, representing the "Presentation of Christ", which is the only pre-iconoclastic exemplar of a religious subject surviving in the city, and a cycle of frescoes of the thirteenth century (found in a chapel at the southeast corner of the building, and painted during the Latin domination) portraying the life of Saint Francis of Assisi.