Fusing multi-source (remote sensing and geophysical) data and diverse approaches validation in targeting hydrothermal alteration and structural anomalies enhances the potential for accurately detecting and characterizing mineralization zones. Sentinel 2 data and ASTER were processed for lithological and hydrothermal alteration mapping in the rare metal-rich Umm Naggat area (Egypt). Different image processing techniques were implemented, including false color composites, minimum noise fraction, band rationing, band math, mineral indices, relative absorption band depth, and constrained energy minimization. The rare metal-bearing Umm Naggat younger granite (NYG) pluton was lithologically discriminated and intra-differentiated to mafic-rich biotite granites, mafic-poor alkali feldspar granites, and albitized granites. Extensive hydrothermal alterations, such as albitization, ferrugination, propylitization, argillization, and phyllitization, overprint the NYG pluton. Normalized standard deviation, automatic lineament extractions, and trend analysis highlighted the key structural directions (NW, NNW, NNE, and NE) and distinguished the NYG pluton as a moderate to high structural density zone. The high structural density and intensive alteration zones are spatially associated and more localized within the NYG pluton than the surrounding rocks. Spatial overlay analysis confirmed that the hydrothermal alterations and fluid circulation systems are structurally-controlled. Furthermore, the hydrothermal alteration mapping and structural analysis outcomes were verified by combining fieldwork, slab polishing, petrographic investigations, and mineral chemistry through semi-quantitative scanning electron microscopy with energy dispersive spectroscopy (SEM-EDS) and quantitative electron probe microanalysis (EPMA) analysis. As a result, the hydrothermal genesis of rare metal-bearing minerals (Nb-rutile, Nb-ilmenite, and columbite) close to or incorporated within alteration minerals (chlorite, muscovite, and hematite) is confirmed from the alteration zones (propylitic, phyllic, and ferruginated). In addition, biotite muscovitization and chloritization significantly contribute to the secondary rare metal enrichment. The current study emphasizes the extensive distribution of secondary rare metal-bearing minerals within the entire NYG pluton (not only limited to the northern albitized granite as depicted by previous studies), which might shed light on these hydrothermally-altered younger granites as a new potential source for Nb and Ta in Egypt.