Ancient metamorphic processes are recorded by the formation of metallic-Pb nanospheres in zircon, a product of internal Pb mobilisation and thermally driven concentration. Here, metallic-Pb nanospheres formed within an ore deposit are characterised for the first time using high-angle annular dark field scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy element-distribution mapping. Exceptional examples from the migmatite-hosted Archean–Paleoproterozoic Challenger Au deposit (Central Gawler Craton, South Australia) support widespread metallic-Pb nanosphere formation in zircon from rocks experiencing granulite-facies metamorphism. We also report new trace-element associations found with metallic-Pb nanospheres and a new mode of occurrence, in which Sc ‘haloes’ form adjacent to metallic-Pb nanospheres within the crystalline zircon lattice. This differs to previously characterised examples of metallic-Pb nanospheres associated with amorphous Si-rich glasses and unidentified Al–Ti, or Fe-bearing phases. Multiple modes of metallic-Pb nanosphere occurrences and trace-element associations suggests multiple modes of formation, probably dependant on zircon composition and metamorphic conditions. Identification of metallic-Pb nanospheres in a growing range of geological settings further highlights the mobility of Pb in zircon and the importance of detailed, nanoscale mineral characterisation, in order to constrain accurate geochronological histories for rocks within high-temperature geological environments.