The Nathenje region in central Malawi hosts significant gold mineralization within high-grade metamorphic rocks of the Mozambique Belt, yet remains underexplored despite extensive artisanal mining activity. The structural controls on primary bedrock gold mineralization within these high-grade metamorphic rocks remain poorly understood, limiting systematic exploration and resource development. We conducted integrated field mapping, structural analysis, petrographic examination, and geochemical sampling to characterize gold mineralization controls in the Nathenje prospect, central Malawi. Detailed structural measurements combined with stereographic analysis reveal three deformation phases, with gold mineralization predominantly associated with D₂ transpressional structures. Fire assay results demonstrate significant gold concentrations (0.15–5.0 g/t Au) in arsenopyrite-bearing quartz veins, with the highest grades systematically occurring at structural complexity zones. Petrographic analysis reveals native gold particles (5–50 μm) intimately associated with arsenopyrite along grain boundaries and within microfractures, indicating coupled precipitation processes. Critically, we identify a hierarchical structural control system operating from regional NE-SW trending shear zones to microscale sulphide boundaries, with fold hinges, dilutional jogs, and amphibolite-gneiss contacts yielding consistently higher gold grades (>3 g/t Au) than other structural settings. Our results establish the first comprehensive structural model for gold mineralization in central Malawi's metamorphic terrain and provide specific targeting criteria applicable to similar high-grade metamorphic environments throughout the East African Orogen.