The Nikeiba composite A-type magmatism of the South Eastern Desert of Egypt is subdivided into two magmatic phases, an older one including syenogranites and alkali feldspar granites, and a younger event characterized by the emplacement of quartz syenites. The older phase has nearly identical chemical composition with high silica contents (SiO2 = 70.7-73.6 wt%), high K2O/Na2O ratios (1.0-1.33), Rb (196.66-241.36 ppm), and low Ba (60.182-279.23 ppm) compared to the younger phase (SiO2 = 65.7-69.5wt%), (K2O/Na2O = 0.70-0.90), Rb (123-172 ppm), Ba (294-717 ppm). These granitoids have elevated total alkalis (9.23-10.2 wt%), similar to alkaline ANS A-type granites characterized by higher concentrations of Zr (821 ppm), Y (135 ppm), Nb (267 ppm), Ga (22.3 ppm), and REEs (up to 639 ppm). They are considered metaluminous to slightly peraluminous post-collisional intraplate A1-type granites, which crystallized from a mixed magma including calc-alkaline I-type tonalites-granodiorites and mantle material by fractional crystallization in the lower to middle crust after lithospheric delamination. The studied granites are rich in rare metals-bearing minerals, including zircon, fluorite, columbite, rutile, apatite, allanite, thorite, fergusonite, and bastnaesite which formed under hybrid conditions. To produce an accurate lithological map of the study area, machine learning algorithms like the Support Vector Machine (SVM) and Random Forest (RF) were applied to the Sentinel-2 data, including both the original bands and bands enhanced using Minimum Noise Fraction (MNF). The SVM applied to the MNF-Sentinel-2 dataset yielded the highest overall accuracy of 92.38 %. It shows excellent performance in the delineation of the studied granites, as verified by field investigations, petrographic, and geochemical data. Moreover, several hydrothermal alteration zones related to rare metals-bearing granitoids, such as sericitization, hematization of ferrous silicates, carbonatization, and kaolinitization, were identified from fused ASTER-Sentinel-2 data. Lineaments and spatial densities were extracted from the Sentinel-1B and ALOS PALSAR radar datasets. Based on the results of the structural analysis, the area is mainly controlled by NW-SE, N-S, and E-W trending fault sets, reflecting the pathways for rare metals enrichment. The cross-link between structural features, hydrothermal alteration zones, and higher density zones detected by combining field investigations, petrography, geochemistry, and remote sensing sheds new light on potentially mineralized zones and proposed exploration targets in the Nikeiba area and similar areas in the Arabian Nubian Shield.