In fact, a few architectural elements within its oldest church (particularly the foundation, which probably dates from the second half of the 5th century) might predate this to even an earlier period. In various histories of the Fayoum Monasteries, it is referred to simply as the Monastery of Naqlun. It is easily seen from a distance, sitting upon an elevated limestone rock on the slope of Gebel al-Naqlun on the edge of the fertile plain some thirteen (to fifteen) kilometers south of Madinat al-Fayoum. The ancient monastery walls of the inner and outer courts are still discernible. Within, the remains of cells and their respective niches can be seen from the roof of the Church of Saint Gabriel.

It would appear from the architectural evidence that the present day church dedicated to the Archangel was largely rebuilt and almost completely redecorated during the latter part of the 19th century, or the beginning of the 20th century, although most of the material used perhaps came from the two earlier churches at Naqlun. Dedicated to Saint Gabriel, it has three haikals, or sanctuaries, with the center most of these, which is semi circular and adorned with small decorative columns, dedicated to the Archangel.

The other two honor the Holy Virgin Mary and Saint George. The church is divided east to west into four sections by wooden screens. These sections include the sanctuaries, the choir (khurus), which is roofed with a cupola, the section for the faithful and the narthex. Both the narthex and the choir appear to date from a later time, and occupy space which was formerly part of the nave. The nave of the church is separated from the side aisles by two ranks of three columns with precious Corinthian capitals which almost certainly date from an older church. On the south side of the nave is a laqqan.