Formed during the Neoproterozoic Era, the Arabian-Nubian Shield (ANS) emerged and is recognized for its rich mineral deposits, establishing it a crucial area for geological exploration. This study investigates three key areas within the ANS situated in the southeastern region of Egypt’s Eastern Desert.: Madari, Sol-Hamed-Malogrem, and Wadi Misah-Gabal Oshkafa. Recently, these areas emerged as potential hotspots for exploring the gold in the southern Eastern Desert of Egypt. Madari exhibits a complex geological landscape characterized by dismembered ophiolites, metavolcanics, metatuffs, quartz diorite enriched with mineralization, syn-tectonic metagabbro-diorites, and granodiorite formations. Gold mineralization within quartz veins highlights the region’s geological diversity, albeit with variable grades and structural patterns. Structural analysis suggests a potential structural control on gold mineralization. Three factors influence the gold mineralization in the area including the source of hydrothermal fluids, the source rocks, and the engine transporting and concentrating the gold deposits. The gold content in different rocks and quartz veins show a higher concentration in the subsurface samples (2.1–21.01 ppm) than in the surface samples (0.00–3.08 ppm), suggesting increase of gold grade with depth. Additionally, the highest gold grade (0.2–2.3 ppm) in stream sediment samples indicates deposition of the gold placer nearby gold-bearing veins which are considered a source for gold mineralization. Gold-silver anomalies indicate that the Mo, Pb, Cu, As, and Sb are potential pathfinders. However, challenges such as variability in mineralization grades within quartz veins and the presence of low-grade felsic porphyry dikes necessitate further exploration and detailed geological studies. Sol-Hamed-Malogrem, situated within the Onib-Sol Hamed suture zone, presents a dynamic geological setting favorable for gold mineralization. The presence of ophiolitic assemblages intruded by gabbros and granites, alongside diverse mineralized structures, suggests multiple mineralizing events. The presence of the alteration types such as silicification, sulfidation, carbonatization, and listwaenitization indicate the occurrence of mineralizing fluids within the alteration zone as an optimistic environment for gold deposition. Gold contents from various sources and from alteration zones range from 0.00 to 5.92 ppm, further suggesting that these sources are favorable for gold deposition. Detailed studies and exploration efforts are essential to understand gold mineralization controls fully. In Wadi Misah-Gabal Oshkafa, a complex geological setting characterized by metavolcanic rocks, pyroclastic formations, and tonalite-granodiorite rocks, alongside quartz veins and dykes, provides promising opportunities for gold exploration. Gold mineralization in the metgabbros is an important target for mining industry. This mineralization is controlled by the composition of the source rock as well as the occurrence of magmatic fluids, the activity of the hydrothermal fluids, and the structural history of the host rock. The dominant NE-SW trending faults, the alteration zones and the vein-type mineralization are favorable for gold deposition. The high gold contents (0.53–16.6 ppm) in metagabbros support its potentiality for gold exploration. However, further exploration and detailed studies are necessary to fully delineate gold mineralization controls, contributing to the area’s potential for mineral resource development and economic prosperity. Overall, these three areas within the Eastern Desert exhibit significant potential for gold exploration and mining activities, highlighting the importance of continued research and exploration efforts to unlock their mineral wealth and contribute to regional development.