Integrating structural control on mineralization and geochemical ore-forming processes is crucial when studying deformed ore deposits. Yet structural and geochemical data are rarely acquired at the same scale: structural control on mineralization is typically investigated from the district to the deposit and macroscopic scales whereas geochemical ore processes are described at the microscopic scale. The deciphering of a deformation–mineralization history valid at every scale thus remains challenging. This study proposes a multiscale approach that enables the reconciliation of structural and geochemical information collected at every scale, applied to the example of the Galat Sufar South gold deposit, Nubian shield, NE Sudan. It gathers field and laboratory information by coupling a classical petrological–structural study with high-resolution X-ray computed tomography, electron back-scattered diffraction and laser ablation inductively coupled plasma mass spectrometry on mineralized sulfide mineral assemblages. This approach demonstrates that there is a linear control on mineralization expressed from the district to microscopic scales at the Galat Sufar South gold deposit. We highlight the relationships between Atmur–Delgo suturing tectonics, microdeformation of sulfide minerals, syn-pyrite recrystallization metal remobilization, gold liberation and ore upgrading. Our contribution therefore represents another step forward in a holistic field-to-laboratory approach for the study of any other sulfide-bearing, structurally controlled ore deposit type.