This study integrates aeromagnetic data with geological information to develop a consistent interpretation of both shallow and deep structural frameworks at various depths in the Missiakat Al Jukh area, located in the Central Eastern Desert, Egypt. The research begins by processing reduced-to-the-north magnetic pole (RTP) anomalies, using Fast Fourier Transformation (FFT) techniques to distinguish between local residual structures and broader regional features. This multi-scale approach enables a more detailed understanding of the geological complexity in the region, revealing its subsurface structures. Advanced geophysical methods such as upward continuation, Euler deconvolution, source parameter imaging (SPI), and global particle swarm optimization (GPSO) were applied to further refine the determination of structural depths, offering critical insights into the distribution and orientation of geological features at varying depths. The study reveals dominant structural orientations aligned in the NNW-SSE, ENE-WSW, north–south, and east–west directions, reflecting the region’s complex tectonic history. This research is of great importance in terms of sustainability. By delivering detailed subsurface maps and providing more accurate depth estimates of basement rocks (between 0.6 and 1.3 km), it contributes to sustainable resource exploration in the region. A better understanding of the geological structure helps minimize the environmental impact of exploration by reducing unnecessary drilling and concentrating efforts on areas with higher potential. Additionally, the use of non-invasive geophysical techniques supports the transition toward more environmentally conscious exploration practices. The integration of these advanced methods promotes a more sustainable approach to mineral and resource extraction, which is crucial for balancing economic growth with environmental preservation in geologically sensitive areas. Ultimately, this work provides a thorough geological interpretation that not only aids future exploration efforts but also aligns with the global push for sustainable and eco-friendly resource management.