The mosque is located inside the monastery, just to the west of the catholicon. The structure was modified in the eleventh century. Originally it seems to have served as the monastery refectory. It is composed of three parts, with access between the three areas by means of large arched openings. In the course of recent renovations, under the plaster there were found crosses carved into the crowns of the arches.

The dominant element in the mosque is minbar, the carved wooden pulpit. This was the donation of Shahan Shah el-Afdal, the powerful chancellor of the Fatimid Empire. The minbar is dated to the month of Rabi I of the year 500, which corresponds to November of AD 1106. Also preserved is a kursi, or prayer stool, given by Abu Mansur Anushtekin, a distinguished emir and luminary of the Fatimid Empire.

The minaret is located opposite the monastery bell tower. It is thought to have been the original belfry of the monastery.