Dair al-Adhra was inhabited by monks until the middle of the 19th century, a fact that is substantiated by various visitors, including Wansleben (1672), F. L. Norden (1740), Richardson (1816), Henniker (1819), and Lord Cursor (1838).

At first glance, the church looks not unlike a modern, massive brick construct with a steeple in the northeast corner. However, it is carved entirely from the rock. The renovation and restoration work carried out in 1938 included the removal of the original stone roof in order to make the church taller so that a second level could be added. Extra rooms were added on the south and west sides. Traditionally, this church is where the local Coptic Christians have their children baptized, and to fill this need, a very large building has recently been built next to the church which contains seven baptismal fonts.

The church itself has a naos, which consists of a nave with two side aisles and a western return aisle, and three sanctuaries. Ten columns hewn from the rock separate the small side aisles and western return aisle. On the south side of the church, the baptismal font has been carved in a column. The area in front of the middle sanctuary, which is raised about one meter above the nave, serves as a Choir (Khurus). The choir is approached by a double flight of steps. Two columns with exquisite Corinthian capitals delineate this space, which prolongs the nave. The central sanctuary is located behind an iconostasis (screen), and is also hew from the rock. It is decorated with small pilasters and niches that are characteristic of ancient Upper Egyptian churches. The small room to the south of the sanctuary was probably the ancient narthex (entrance area), and is thought to be the oldest part of the church.

Above the west entrance friezes from ancient Christian edifices in the area present motifs drawn from the vegetable and animal realms. One, which shows seven human figures, is especially interesting. Each of the these are depicted within a niche, and holding a book in the left hand. These human figures probably represent seven apostles, and were once a part of a larger composition, the rest of which is now lost.

The Church of the Holy Virgin is the goal of a pilgrimage which attracts annually tens of thousands of pilgrims who come by feluccas, trains, buses and other transport from all over Egypt for the Feast (Moulid) of the Assumption of the Holy Virgin, which is celebrated on August 22nd.