Opening up greenfields regions for mineral exploration programs is facilitated through understanding their mineral prospectivity. The Capricorn Orogen in Western Australia can be considered such a greenfields-dominated region, that hosts several mineral occurrences or deposits, but only a few have been mined extensively. Mineralisation in much of the Capricorn Orogen can be related to basin development, inversion and orogenesis during the Paleoproterozoic. Extension, on a regional scale, dominates the tectonic processes observed in the area through time and is interspersed by periods of contractional orogenesis, including the 2005–1950 Ma Glenburgh and 1830–1780 Ma Capricorn orogenies. Prospectivity models for base metals and gold in the northern and southern parts of the Capricorn Orogen suggest there is a spatial link between potentially prospective zones and the Archean basement, but also between the base metal and gold mineral systems. One of these links is tied to the control of the deep crustal-scale tectonic architecture over basin development and subsequent inversion during orogenesis. This early architecture contributed towards the preservation of mineralisation by protecting the area from tectonothermal processes such as deep burial and metamorphism. In addition, the spatial concurrence of zones prospective for the c. 2 Ga Au-Cu volcanic massive sulphide and c. 1.8 Ga orogenic Au style mineralisation in the northern part of the Bryah Sub-basin suggests a spatial link between the two mineral systems, while supporting the hypothesis that deposition of different ore styles is driven by long-lasting, regional geodynamic processes. In the Capricorn Orogen, these changing conditions reflect the transition from a plate-margin setting to an intraplate setting.