The Church of the Virgin Mary was built in the same location in which the Holy Family resided. Next to the church was a bath, built according to the Roman system. Later on, a monastery was established which was called Monastery of Baptism, and it remained full of monks until the end of the twelfth century AD.
The church was restored in the eleventh century by order of the Fatimid Caliph Al-Hakim be Amr Allah, and in the sixteenth century the church was destroyed and remained in ruins until Muhammad Ali Pasha ordered its reconstruction in 1846 AD, while preserving its ancient character and preserving the remaining archaeological parts.
In 1968 the nave was rebuilt, and during the construction process the relics of some saints were found, including the Patriarch Anba Sawirus of Antioch and Anba Zacharias, Bishop of Sakha in the seventh century AD, along with his remains.
The church suffered an unfortunate fire incident on June 18, 2008; this resulted in the complete burning of a number of antiquities in the church, including the ancient iconostasis of the sanctuary; and a rare icon of the Virgin Mary.
It was renovated according to the Coptic architectural heritage in very precise and beautiful geometric and artistic ways, as special-type bricks were used during its construction and renovation, and it was open in May 2014.
The iconostasis or “icon holder” is in front of the ancient part of the church, which consists of 3 sanctuaries. The middle sanctuary is in the name of the Virgin Mary, whose construction dates back to the fourth century AD, and it is still present until now. It was raised twice: the first time in the eleventh century and the second time in the nineteenth century AD.