The monastery is 2 acres and 16 carats. Prince Omar Toson was the first to measure its area and the height of the outer wall, the fortress and the mill. He documented all of that in his book in 1935 AD.
Saint Bishoy established the monastery that holds his name in the fourth century after 374 AD.
In 340 AD St. Bishoy was ordained monk and lived in the wilderness of Wadi Al Natron in an area called Abu Henes hill, 3 km south east the present monastery. He and St. John the short were disciples of St. Bemwah.
In 374 AD St. Bemwah died.. An angel appeared to St. John the Short and to St. Bishoy, the angel told St. John to live beside the tree of obedience and told St. Bishoy to live at the west side of Abu Henes hill in a cell which exists till today at Virgin Mary Syrian Monastery.
Shortly he became well known and had many disciples, they built the ancient church of St. Bishoy, dug a well known as “the well of Martyrs” and built a mill for grinding grains. This was the beginning of St. Bishoy monastery, everything was peaceful until the Berbers attack in 407 AD.
St. Bishoy left the monastery with his disciples and went to Ansana (Menya Governorate) where he established another monastery by his name in Dayr Bersha. In 417 AD. he passed away and was honourably buried there.
In 840 AD. Ahmed Ibn Tulun was able to conquer the Berbers, then later the monks began to build a wall for the monastery that took three years to complete.
In 843 AD. the monks of St. Bishoy monastery asked Pope Yosab, the fifty one Patriarch to bring the body of St. Bishoy back from Ansena to his monastery.
In the thirteenth century the white ant attacked the monastery and destroyed the ceiling of the ancient church as it was made of wood>
In the Fourteenth century, Pope Benjamin the 2nd built a new ceiling using stones.
Therefore the ancient church is dated to the fourth century, while its ceiling is dated to the fourteenth century. Through years everything was peaceful , despite the monastic and architectural progress of the monastery was very slow until November 1971 when H.H. Pope Shenouda the 3rd was enthroned 117th Patriarch of Alexandria, he made a great monastic and Architectural renaissance at St. Bishoy monastery. H.H. built many churches, buildings of service, and the papal residence inside the monastery. When H.H. established the Papal Logos Centre. He also held many cultural conferences, and encouraged the monks to study, research and learn different languages.