World-class magmatic mineral systems are characterised by fluid/melt originating in the deep crust and mantle. However, processes that entrain and focus fluids from a deep-source region to a kilometre-scale deposit through the crust are unclear. A magnetotelluric (MT) and reflection seismic program across the margin of the Gawler Craton, Australia yield a distinct signature for a 1590 Ma event associated with emplacement of iron-oxide copper gold uranium (IOCG-U) deposits. Two- and three-dimensional MT modelling images a 50 km wide lower-crustal region of resistivity <10 Ωm along an accreted Proterozoic belt. The least resistive (~1 Ωm) part terminates at the brittle-ductile transition at ~15 km, directly beneath a rifted sedimentary basin. Above the brittle-ductile transition, three narrow low-resistivity zones (~100 Ωm) branch to the surface. The least resistive zone is remarkably aligned with the world-class IOCG-U Olympic Dam deposit and the other two with significant known IOCG-U mineral occurrences. These zones are spatially correlated with narrow regions of low seismic reflectivity in the upper crust, and the deeper lower-crust conductor is almost seismically transparent. We argue this whole-of-crust imaging encapsulates deep mineral system and maps pathways of metalliferous fluids from crust and mantle sources to emplacement at discrete locations.