Seat of Coptic Pope

By the 11th century A.D., the church served as the Seat of the Coptic Orthodox Pope of Alexandria, which is historically based in Alexandria, Egypt. But as ruling powers moved away from Alexandria to Cairo after the Arab invasion of Egypt during Pope Christodolos 's tenure, Cairo became the fixed and official residence of the Coptic Pope at the Hanging Church in Cairo in 1047.

Infighting between the Church of Saints Sergius and Bacchus and the El Muallaqa Church broke out due to the wishes of that patriarch's desire to be consecrated in the Hanging Church, a ceremony that traditionally took place at Saints Sergius and Bacchus.