The current phosphate mine wastes at El-Liffiya-Maghrabi sector, Abu-Tartur plateau, are represented by low-grade phosphorites along with overburden of glauconite and shale deposits. Although phosphorites contain sufficient concentrations of the valuable plant-nutrients (e.g. 18.29 wt% P2O5, 35.29 wt% CaO, and 14.43 wt% SO3), it holds unallowable levels of some toxic heavy metals (e.g. 45.8 ppm As, 26.1 ppm Cd, 180 ppm V, and 52.3 ppm U). This in turn constrains the potential agronomic application of such deposits as being nature-disturbing materials. On the other side, contents of such metals in the overburden are lower than phosphorites (e.g. 9.1–15.1 ppm As, 0.2–2.4 ppm Cd, 0.4–1.2 ppm U, and 102–172 ppm V). Consequently, mixing phosphorite with its overburden was followed as a procedure to decline the contents of heavy metals and to valorize the nature-disturbing mine wastes as a potential rock-based fertilizer and soil conditioner. The mixing process was performed at different four ratios of 1phosphorite: 1glauconite: 1shale “M#1″, 2phosphorite: 1glauconite:1shale “M#2″, 1phosphorite: 2glauconite:1shale “M #3″ and 1phosphorite: 1glauconite:2shale “M#4". The agronomic potential of each rock mixture was studied using petrography microscope, XRD, XRF, ICP-MS, UV–visible spectrophotometer, and flame photometer. The evaluation study depended mainly on contents of macro- and micro-nutrients (e.g. P, K, Ca, Mg, S, Mn, Cu …. etc), levels of toxic heavy metals (e.g. As, Cd, U, and V), organic carbon content, organic-acid solubility, H2O2-driven solubility, and cation exchange capacity “CEC”. The overall results revealed that the prepared mixtures, in particular M#4, can serve as a rock-based fertilizer rich in plant-nutrients at comparable levels with other highly reactive phosphorites of the Hamrawein mine (Egypt), North Carolina, Morocco, and Germany. Also, the heavy metal contents were noticeably reduced to acceptable limits (e.g. 15 ppm As, 1.3 ppm Cd, 3 ppm U, and 110 ppm V) that are recommended by the German Fertilizer Ordinance, Kenya Standards for soluble compound fertilizers, and the Canadian Food Inspection Agency. On the other hand, organic carbon contents (2.01–2.25 wt% C) along with CEC values (68–72 meq/100 g) support the application of the prepared waste mixtures as a soil conditioner.