The Rajapalot area of Finnish Lapland hosts an unusually high-grade association of cobalt-only and gold–cobalt deposits (10.91 Mt @ 2.5 g/t Au + 0.44% Co total inferred resources) within multiply folded metasedimentary rocks of the Paleoproterozoic Svecofennian collisional orogeny. Through the integration of X-ray computed micro-tomography and micro-X-ray fluorescence raster imaging of drill-core samples, we produce a model of cobalt-bearing ore mineralisation, which reveals primary fluid transportation mechanisms and precipitation pathways. When combined with the deposit-scale, high-resolution ground-based magnetic geophysical data, we show that cobalt-bearing ores in the Rajapalot region occur mostly as saddle reefs located in dilated fold hinges, which formed by simultaneous synthetic and antithetic shearing along developing crenulation-cleavage planes and incompetent bedding layers, respectively. We suggest that multi-layered rock complexes with alternations of competent and incompetent layers deformed and metamorphosed to upper greenschist-lower amphibolite facies should represent focus regions for cobalt exploration targeting campaigns in orogenic belts. The non-destructive workflow presented in this study could be an integral part of an early stage of cobalt mineral processing and traceability before metallurgical treatment.