Beryl mineralization in the Nugrus-Sikait domain in the South Eastern Desert (SED) of Egypt occurs as disseminated crystals in granitic pegmatite and quartz, as well as pegmatite veins crosscutting mélange schist and ophiolitic rocks. When granitic pegmatite comes into contact with the ophiolitic rocks, phlogopite and amphibole schists are formed due to K metasomatism. The ophiolitic mélange is intruded by leucogranite and related pegmatite along the NNW to NW Nugrus shear zone. Beryl samples have been collected from Um Sleimat, Madinat Nugrus, Wadi Abu Rusheid, and Wadi Sikait. Major oxides and in situ trace and rare earth elements (REEs) of beryl and associated minerals were analyzed through EPMA and LA-ICP-MS, respectively. The investigated beryl, based on its color and chemical compositions, can be classified into the two following types: pegmatitic beryl (type I) and schist-related beryl (type II). The former is colorless to pale green, and is mainly restricted in pegmatite veins; it is poor in Cr2O3 (up to 0.03 wt%) and MgO (Nil). The latter, deep green in color, is rich in Cr2O3 (up to 0.27 wt%) and MgO (up to 2.71 wt%), and occurs within quartz veins, phlogopite schists, and tremolite schists. The abundant beryl mineralization in phlogopite schists and their related quartz veins suggests that granite and associated pegmatite are the source rocks for the Be-bearing fluids that migrate along the NW-SE trending deep-seated tectonic zone, such as the Nugrus shear zone. Therefore, the formation of beryl in schists is attributed to the interaction of granitic/pegmatitic-derived Be-bearing fluids with serpentinite and gabbro interlayered with mélange schists. Variations in the trace and REE contents of both beryl types (I and II) indicate their two-stage formation from different compositions of Be-rich fluids, where light REEs, Zr, Nb, Ba, and Th decrease from type I beryl to type II. These two phases of beryl could be attributed to the magmatic/hydrothermal fluids associated with the pegmatite emplacement. The early phase of the late-stage magmatic-derived fluids was closely related to magma evolution and pegmatite formation, forming euhedral type I beryl. The late phase of pegmatite-derived fluids was mixed with serpentinite/schist-derived fluids that cause high V and Cr content in type II beryl. The composition of parent magmas of felsic rocks, the high degree of magma fractionation or the late stage melts, fluid compositions (rich in Be, Li, Cs, Rb, K), and alkali metasomatism, as well as the linear NW-SE trending deep-seated shear zone, are all factors possibly influencing beryl mineralization in the SED of Egypt.