Little of the original monastery remains. However, during the sixth century, a community of women associated with St. Rachel also settled within the structures and a new period of building began. The monastery appears to have actually reached its zenith during the seventh century, when there were as many as five thousand monks. After the Arab conquest of Egypt during the seventh century AD, the population of the monastery slowly declined until from the tenth (or eleventh) century on, there were apparently no monks left to hold back the sands of the desert, which now cover most of the deserted buildings.

The Bawit complex, though mostly gone now, is known the world over because of the abundance of architectural and painted decorations that were recovered there. Many of these items now reside in either the Louvre Museum in Paris, or in the Coptic Museum in Cairo. Excavations of this monastery were carried out by French archaeologists during the early part of the twentieth century. This work revealed at least two churches and other groups of buildings, along with parts of walls. Judging from the enclosure walls, the monastery was enormous, as they stretched on for some three kilometers in length. The two churches discovered at the center of the complex were simply termed the "north" and "south" churches. We appear to have little information on their dedication.

However, the south church has been mostly freed from the sand and even partially reconstructed. Engraved text, apparently on the lintel to an entrance, associates the archangels Michael and Gabriel with the founding fathers of the monastery (Apollo and his companion, Abbot Phib). It was apparently built during the sixth century over an earlier edifice from the fourth century. The earlier structure was perhaps not a place of worship at all, while the second structure presents all the characteristics of a basilica church, with a nave, two side aisles, a sanctuary with a niche, and the entrance on its south and north sides. At one time, there were decorations carved in stone and wood and painted friezes with geometrical, vegetal and figurative motifs that ran along the interior and exterior walls of the building. The nearby north church seems to date from the eighth century, and like the south church, appears to be a transformation of a previous building.

However, for some reason, the archaeological work on the monastery was abandoned in about 1913. Since then, little or no research has been conducted on this, one of Egypt's great monasteries. Even the early work lacks satisfactory written and photographic documentation. In 1976, apparently a number of wall paintings were discovered at the site during unprofessional excavations, which were subsequently transported to the Coptic Museum. No report was provided detailing this discovery.