In the northern part of the Bahariya Depression (Western Desert, Egypt) the Eocene carbonate succession, unconformably overlying the Cretaceous deposits, consists of three main stratigraphic units; the Naqb, Qazzun and El Hamra formations. The Eocene carbonates are relevant as they locally host a large economic iron mineralization. This work revises the stratigraphic attribution of the Eocene formations on the basis of larger benthic foraminifers from both carbonate and ironstone beds. Eight Nummulites species spanning the late Ypresian e early Bartonian (SBZ12 to SBZ17) were identified, thus refining the chronostratigraphic framework of the Eocene in that region of Central Egypt. Moreover, additional sedimentological insight of the Eocene carbonate rocks is presented. The carbonate deposits mainly represent shallow marine facies characteristic of inner to mid ramp settings; though deposits interpreted as intertidal to supratidal are locally recognized. Dating of Nummulites assemblages from the youngest ironstone beds in the mines as early Bartonian provides crucial information on the timing of the hydrothermal and meteoric water processes resulting in the formation of the iron ore mineralization. The new data strongly support a post-depositional, structurally-controlled formation model for the ironstone mineralization of the Bahariya Depression.