Discovering ore deposits is becoming increasingly difficult, and this is particularly true in areas of glaciated terrains. As a potential exploration tool for such terrains, we test the vectoring capacities of trace element and sulfur isotope characteristics of pyrite, combined with quantitative statistical methods of whole-rock geochemical datasets. Our target is the Rajapalot gold–cobalt project in northern Finland, where metamorphosed Paleoproterozoic volcanic and sedimentary rocks of the Peräpohja belt host recently discovered gold prospects, which also have significant cobalt enrichment. The focus is particularly put on a single gold–cobalt prospect, known as Raja, an excellent example of this unusual cobalt-enriched gold deposit, common in the metamorphosed terranes of northern Finland. The major lithologies at Rajapalot comprise amphibolite facies metamorphosed and polydeformed calcsilicate rocks that alternate with albitic units, mafic volcanic rocks, mica schist and quartzite. Mineralization at Rajapalot prospects is characterized by an older Co-mineralizing event and a younger high-grade Au mineralization with re-mobilization and re-deposition of Co. Detailed in situ laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful technique that produces robust trace element and sulfur isotope databases from paragenetically and texturally well-characterized pyrite from the Raja prospect. The results are treated with appropriate log-ratio transformations and used for multivariate statistical data analysis, such as the computation of principal components. Application of these methods revealed that elements such as Co, Ni, Cu, Au, As, Ag, Mo, Bi, Te, Se, Sn, U, Tl and W have high vectoring capacities to discriminate between Co-only and Au–Co zones, as well as between mineralization stages. The systematic pyrite study suggests that homogenous sulfur isotopic characteristics (+1.3 ‰ to +5.9 ‰) and positive loadings of Co, Se, As, Te, Bi and Au onto PC1 are reflective of an early stage of Co mineralization, while the opposing negative loadings of Mo, Ni, W, Tl, Cu and Ag along PC1 are associated with pyrites from the Au-mineralizing event. The sulfur isotopic signature of the latter pyrite type is between −1.2 ‰ and +7.4 ‰. Subtle patterns recognized from the whole-rock geochemistry favor an As–Au–Se–Te–W–U signature along the positive axis of PC1 for the localization of high-grade Au–Co zones, whereas the element group Ni, Cu, Co, Te, Se and As, which has negative loadings onto PC2, will predict Co-only zones. This study shows the efficiency of trace element geochemistry in mineral exploration targeting, which has the capacity to define future targets by characterizing the metallogenic potential of a host rock, as well as distinguishing various stages of mineralization.