The most eastern monastery in Wadi al-Natrun, it was founded by a monk by the name of Bishoi who was a disciple of St. Macaruis of the nearby monastery. St. Bishoi was born in the Nile Delta in 320 AD. He became a monk at the age of 20. His relic is in the monastery, and the monks claim that it is still intact. Every July 17, his casket is carried around the church. The monastery is the official residence of the Coptic Pope Shenouda III, who, like several former Coptic popes, was originally from this monastery.

Deir Anba Bishoi contains five churches; one used on a regular basis ,one used in summer only, one used in winter only, two that aren’t used at all.

The wall of the monastery’s churches are painted with murals of the disciples, the apostles and Coptic saints. There is a carved wooden door that dates to the 12th century. The ancient refectory is a long narrow room with vaulted ceiling. It has been turned into a museum. The acoustics in this room are said to be remarkable.

The monastery includes cells for monks, retreat houses, a residence for the Coptic Pope, annexes for a reception area, an auditorium and conference rooms. It is the only monastery open to the public and it housed about 24 monks.