This study investigates the internal and external structures of the Morro São João Alkaline Complex, located in Southeast Brazil, using high-resolution aeromagnetic geophysical data. The primary objective is to delineate the architecture of the underlying magma chamber system. The geophysical investigation primarily employs aeromagnetic data processing techniques, unveiling subsurface structures and shedding light on the magmatic evolution of the region. Aeromagnetic data from the Rio de Janeiro Aerogeophysics Project were processed and interpreted to identify significant magnetic anomalies and structural features. The results reveal five distinct magnetic domains correlating with various lithologies, including Monzogranite and Amphibolite Paragneiss. The observed NW-SE and NE-SW magnetic lineaments are crucial indicators of the region’s structural complexities, reflecting tectonic influences and highlighting the significance of regional geological context in deciphering magnetic anomalies. The geophysical anomaly associated with Morro São João, characterized by its rounded shape and eccentricity, aligns with the documented lithological variations. Numerical inversion techniques were employed to create a detailed three-dimensional model of the magmatic system. The main geophysical result is the 3D inversion model, which unveils a magmatic chamber approximately 4 km beneath the surface. This model reveals the subsurface architecture and conduits from the chamber, providing a dynamic perspective on the processes shaping the hill’s morphology. The integration of regional magnetic lineaments, lithological variations, and the 3D inversion model elevates our comprehension of the geophysical intricacies of the Morro São João Alkaline Complex.