The church was founded in 1417 during the reign of Pope Gabriel V, the 88th Patriarch of the See of St. Mark in Alexandria and the late Anba Basilius, Bishop of Qus and Naqada.  

St. Mary Church was the seat of the diocese and the residence of at least 10 successive bishops from 1517 until 1839.  These bishops are: 

Anba Bedir, bishop of Qus and Naqada, Anba Mikhail, Bishop of Naqada, Anba Khristodoulo I, Bishop of Naqada, Anba Mikhail II, Bishop of Naqada, Anba Khristodoulo II, Bishop of Naqada, Anba Youannis, Bishop of Naqada, Anba Morcos, Bishop of Naqada, Anba Boutros, Bishop of Naqada and Gerga. Anba Makarios I (Makara) and Anba Makarios II 

Because it was the only church at that time until the beginning of the 20th century, all priests from the monasteries took turns celebrating liturgies there on a daily basis, especially during Lent and other church fasts.  The church has eight altars. 

Many patriarchs visited this church including Pope Youannis XII and Pope Kyrillos V. 

The church was restored by all bishops. The most important restorative works were: 

1. A comprehensive restoration during the reign of Anba Makarios I (Makara) in 1802. 

1. A comprehensive restoration and re-inauguration in January 2003 in the pontificate of H.G. Bishop Biemen, the current bishop of the diocese, may God prolong his life.