After the Ayyyubid conquest in 1187, the church and monastery were transformed into a Muslim school. The bishops were only able again to occupy it again briefly when the city was in Christian hands between the Sixth Crusade (1229) and the Khwarazmian conquest (1244). Thereafter the Syriac Orthodox used the small church of Saint Thomas of the Germans until it was handed over to the Muslim authorities by the incumbent monk, who converted to Islam in 1451/1452.