The Gebel Abu Hamamid area forms the middle part of Shadli Metavolcanics Belt of the South Eastern Desert, which hosts the largest volcanogenic massive sulfide deposits in Egypt. The host-rock succession belongs to the Younger Hamamid Metavolcanics (YHM) group, consisting of mafic and felsic lavas with variable volcaniclastics. Although several studies have attempted to clarify the crustal evolution of the Neoproterozoic basement rocks of the South Eastern Desert, researchers have yet to develop a deep understanding of the petrogenesis, tectonic setting, and ages of these host rocks. In the current study, we newly report whole-rock geochemistry, mineral chemistry, and in-situ U–Pb zircon dating from basaltic to rhyolitic rocks of the YHM group to describe their magmatic evolution. Results indicate that the mafic rocks are characterized by tholeiitic affinity and arc-like geochemical signatures with significantly enriched large-ion lithophile elements and depleted high field strength elements. The parental magma was likely generated by partial melting (~10–15%) of a spinel-lherzolite source mantle that was metasomatized by fluids from a former subduction event, followed by magma ascent under low pressure and low oxygen fugacity conditions. The felsic lavas (~695 Ma) are characterized by subduction-related geochemical characteristics with significant enrichments in Zr, Hf, and Sm. They formed from lithosphere-derived magma enriched by melts from the ancient subducted slab, and later experienced an assimilation-fractional crystallization (AFC) process. The YHM group was formed under extensional geodynamic conditions (back-arc basin setting). The zircon grains display hydrothermal overgrowth at the rims, most likely due to regional metamorphic and hydrothermal changes. This characteristic is likely the effect of hydrothermal fluids associated with the Jurassic-Cretaceous tectonothermal event in the South Eastern Desert.