Some accounts go that the church was built on the ruins of a place where the Holy Family (the Virgin Mary, Christ the Child, and Saint Joseph the Carpenter) took refuge during the three years they spent in Egypt, according to the Bible, to escape from Herod, the ruler of Palestine, who had ordered the killing of children for fear of a prophecy received. Some see it as a place for a cell (a place of seclusion) in which one of the hermit monks lived, in one of the rocky vaults excavated in the place.

The church was renewed several times during the Islamic era, once during the Caliphate of Harun al-Rashid when the patriarch Anba Morcos asked the governor for permission to renew the church. And once during the reign of Al-Aziz Billah the Fatimid, who allowed Patriarch Ephraim the Syriac to renovate all the churches of Egypt and repair what had been destroyed. And the third time in the era of El-Zaher La`ezaz Din Allah.

The church has been the seat of many patriarchs since the eleventh century, and Patriarch Christodoulos was the first to take the Hanging Church as the seat of the Pope of Alexandria, and a number of patriarchs were buried there in the eleventh and twelfth centuries, and there are still pictures and icons of them in the church that lit candles. And the trails of priests, bishops, and the trials of heretics were held there as well, and it is considered an important shrine for the Copts, due to the historical antiquity, the connection of the place with the Holy Family, and its presence among churches and monasteries of venerable saints, so it is easy to visit them as well.