Ophiolitic peridotites exposed in the Eastern Desert (ED) of Egypt record multiple stages of evolution, including different degrees of partial melting and melt extraction, serpentinization, carbonatization and metamorphism. The present study deals with metaperidotites at two selected localities in the central and southern ED, namely Wadi El-Nabá and Wadi Ghadir, respectively. They represent residual mantle sections of a Neoproterozoic dismembered ophiolite that tectonically emplaced over a volcano-sedimentary succession that represents island–arc assemblages. The studied metaperidotites are serpentinized, with the development of talc-carbonate and quartz-carbonate rocks, especially along shear and fault planes. Fresh relics of primary minerals (olivine, orthopyroxene and Cr-spinel) are preserved in a few samples of partially-serpentinized peridotite. Most of the Cr-spinel crystals have fresh cores followed by outer zones of ferritchromite and Cr-magnetite, which indicates that melt extraction from the mantle protolith took place under oxidizing conditions. The protoliths of the studied metaperidotites were dominated by harzburgites, which is supported by the abundance of mesh and bastite textures in addition to some evidence from mineral and whole-rock chemical compositions. The high Cr# (0.62–0.69; Av. 0.66) and low TiO2 (<0.3 wt%) contents of the fresh Cr-spinels, the higher Fo (89–92; Av. 91) and NiO (0.24–0.54 wt%, Av. 0.40) contents of the primary olivine relics, together with the high Mg# (0.91–0.93; Av. 91) and low CaO, Al2O3 and TiO2 of the orthopyroxene relics, are all comparable with depleted to highly depleted forearc harzburgite from a suprasubduction zone setting. The investigated peridotites have suffered subsequent phases of metasomatism, from ocean-floor hydrothermal alteration (serpentinization) to magmatic hydrothermal alteration. The enrichment of the studied samples in light rare earth elements (LREEs) relative to the heavy ones (HREEs) is attributed to most probably be due to the contamination of their mantle source with granitic source hydrothermal fluids after the obduction of the ophiolite assemblage onto the continental crust. The examined rocks represent mantle residue that experienced different degrees of partial melting (~10% to 25% for W. El-Nabá rocks and ~5% to 23% for W. Ghadir rocks). Variable degrees of partial melting among the two investigated areas suggest mantle heterogeneity beneath the Arabian-Nubian Shield (ANS).