In 912 the Fatimids sacked the town of Ajdabiya and destroyed the mosque building a new one on the site. The Fatimid mosque consists of a rectangular structure (47 by 31 m) built out of mud brick with corners, piers, jambs and other structurally important points built out of stone. There was one entrance in the north-west side opposite the mihrab and several other side entrances, all of which appear to have been plain in contrast to the monumental porches at Mahdiya and Cairo. Inside there is a large courtyard paved with flagstones and a water tank in the middle at the northern end of the mosque. The courtyard is surrounded by arcades and on the south-eastern side is the sanctuary. The latter has a wide central aisle running at right angles to the qibla wall where it meets a transept running parallel to the qibla wall; all the other aisles arc aligned at right angles to the qibla.

To the left of the main entrance is a large square block 4 m high which was the base of a minaret with an octagonal shaft. This is the earliest example of this type of minaret which was later developed into the characteristic Cairene minaret form. There are also traces of a staircase built into the wall which have been interpreted as the remains of a staircase minaret used before the erection of the later octagonal one.