Egypt’s mineral resources are an effective means of raising the country’s income. Consequently, searching for deep subsurface ore deposits is essential. In this study, we map the subsurface structure and the occurrence of related gold-ore mineralization deposits in ophiolitic-assemblage rocks around the Wadi El-Saqia area in the Central Eastern Desert of Egypt. Our approach combines airborne geophysical data (aeromagnetic mapping) and geochemical analyses. We enhanced the aeromagnetic data and interpreted them using edge-detection methods, such as the first-order vertical derivative (FVD), the analytic signal (AS), the total horizontal derivative (THD), the tilt derivative (TD), the tilt angle (TA), the theta map, both grid and porphyry analyses from the Centre for Exploration Targeting (CET), and Euler deconvolution (ED) techniques. Utilizing these methods, we located the main structural lineaments/contacts that control the distribution of hydrothermal alteration zones. In addition, our geochemical analyses use the mineral chemistry of pyroxene and plagioclase to describe their tectonic and magmatic evolution. The airborne geophysical results revealed that NW–SE, NE–SW, N–S, and E–W structural orientations are prevalent in the studied area, with depths ranging from less than 50 m to about 600 m. To validate the findings, we carried out geochemical sampling, which indicates that pyrite, galena, pyrrhotite, and electrum contain good percentages of gold (ranging from 0.01–0.09 wt%, 0.03–0.1 wt%, 0.12–0.14 wt%, and 53.55–55.01 wt%, respectively). In this study, we were thus able to find preferred locations for gold mineralization, which highlights the value of combining aeromagnetic and geochemical data for mineral exploration.