Shortly after the Fall of Constantinople the building was converted into a mosque, and the monastery was converted for a while into a Medrese. The Ottomans named it after "Molla Zeyrek", a scholar who was teaching there. However, due to its importance in Byzantine history, Zeyrek was one among the few buildings of Istanbul whose ancient denomination was never forgotten. Among others, the church of Pantokrator is remembered by Pierre Gilles in his classic work about Constantinople, written in the sixteenth century. After the completion of the Medreses in the Fatih complex in 1471, the students abandoned Zeyrek, and the rooms of the monastery occupied by the Medrese vanished later.