Deir Abu Magar, also called Deir Anba Makaryus after its 4th century founder St Macarius the Great was probably the first monastery in Wadi al-Natrun. In the 6th century, the Byzantine rulers mandated that the Coptic Patriarchs no longer reside in Alexandria and Deir Abu Magar became the seat of the Coptic Church. Most of the present monastery was rebuilt by Pope Shenudah (859-81) after it was attacked and heavily damaged for the third time in 866. By the end of that century, the tower's outer walls were reinforced, and the outer defensive wall was built. Once only housing 6 monks, the monastery is today the richest in Wadi al-Natrun. There are more than 100 monks and 600 workers in the extensive cattle and dairy farm.

The main church and the oldest ion the monastery is the Church of St. Macarius has icons from the 4th and 5th centuries and frescoes from the 10-11th C. The qasr (Keep) has been converted to three chapels: the Chapel the Virgin, the Church of St Anthony and the Church of Archangel Michael, and the Churchof the Travelers (al- Sawwah).

It was the usual habit after a patriarch had been elected and consecrated to the See of St. Mark in Alexandria, that he would be ordained and sanctified in this monastery. Many patriarchs were ordained in this monastery, and many of them are buried here.