This study provides an in-depth geophysical interpretation of the gold and base metal mineralisation of the Ibaga area related to hydrothermal alteration using high-resolution aero-geophysical and induced polarisation ground survey datasets. Despite its potential for gold and base metal and the available artisanal mines, the Ibaga area has remained poorly understood on geophysical signatures of ore deposits and other subsurface geological structures controlling the mineralisation. The magnetic results on the major structures show high magnetic signatures, supported by gravity, radiometric signatures and petrophysical analysis. The potential mineralised structures are interpreted as dyke for gold, and contacts for copper and the depth to the basement varies from 0.113 to 1.556 km. The gravity anomaly shows high values on the gold mineralisation similar to high-density values of dolerite dykes and gabbro and low to medium radiometric concentrations associated with mineralised zones. The magnetic signatures on the copper deposits coincide with the relative positive gravity anomaly of high-density intrusive bodies and relatively moderate conductive bodies with elevated potassium (K) alteration. The copper deposit also has intermediate K and low to intermediate K/Th and K/U ratios caused by K alteration within the geological structures. The good spatial correlation of the hydrothermally altered zones, igneous intrusions and geological structures implies that the geological features associated with gold and copper mineralisation lie within the regions of high-density intrusive bodies and geological structures (faults, fractures and dykes). These features are also associated with relatively moderate conductive bodies, low to intermediate radiometric concentrations and low to moderate magnetic signatures. Thus, the study reveals that the delineated geophysical signatures on gold and base metal mineralisation are associated with quartz–sericite–muscovite ± chlorite hydrothermally altered areas, deformed structures, and intrusive bodies, which act as pathways for the migration and accumulation of hydrothermally altered fluids.