The enigmatic botryoidal nuggets of platinum (Pt) and palladium (Pd) from Córrego Bom Sucesso in the southern Serra do Espinhaço, Minas Gerais, Brazil, are considered to have formed during supergene alteration of placer deposits. This requires hitherto unidentified precious-metal enrichment processes and is inconsistent with Pt–Os age of 180 Ma that entails formation at depth, as recently proposed. Here we report the first mercury (Hg) and helium (He) isotopic determinations of Pt–Pd nuggets. Mercury isotopic compositions have a mass-independent fractionation (MIF) signature with an odd-mass deficit (Δ¹⁹⁹Hg = − 0.22 ± 0.04; 1SD, n = 15), which requires aqueous photochemical reduction of Hg (II). Extremely low ³He/⁴He (<0.001 R_a) and extremely high concentrations of He (up to 1.9 × 10¹⁷ at/g) are indicative of nugget formation from He-enriched fluids within the quartzite sequence of the Espinhaço basin, not from meteoric surface water. The data are consistent with a nugget-forming setting in the deep biosphere, as a result of groundwater interaction with Pt–Pd–Hg minerals in Pan-African-Brasiliano post-orogenic veins. We propose that the negative Hg-MIF signature was inherited from the vein minerals that originally acquired their Hg from Earth's surface during the intracratonic sedimentation of the Proterozoic Espinhaço basin.