Carbonate rocks frequently undergo remagnetisation events, which can partially/completely erase their primary detrital remanence and introduce a secondary component through thermoviscous and/or chemical processes. Despite belonging to different basins hundreds of kilometres apart, the Neoproterozoic carbonate rocks of South America (over the Amazon and São Francisco cratons) exhibit a statistically indistinguishable single-polarity characteristic direction carried by monoclinic pyrrhotite and magnetite, with paleomagnetic poles far from an expected detrital remanence. We use a combination of classical rock magnetic properties and micro-to-nanoscale imaging/chemical analysis using synchrotron radiation to examine thin sections of these remagnetised carbonate rocks. Magnetic data shows that most of our samples failed to present anomalous hysteresis properties, usually referred to as part of the “fingerprints” of carbonate remagnetisation. Combining scanning electron microscopy-energy-dispersive X-ray spectroscopy (SEM-EDS), highly sensitive X-ray fluorescence (XRF), and X-ray absorption spectroscopy (XAS) revealed the presence of subhedral/anhedral magnetite, or spherical grains with a core-shell structure of magnetite surrounded by maghemite. These grains are within the pseudo-single domain size range (as well as most of the iron sulphides) and spatially associated with potassium-bearing aluminium silicates. Although fluid percolation and organic matter maturation might play an important role, smectite-illitisation seems a crucial factor controlling the growth of these phases. X-ray diffraction analysis identifies these silicates as predominantly highly crystalline illite, suggesting exposure to epizone temperatures. Therefore, we suggest that the remanence of these rocks should have been thermally reset during the final Gondwana assembly, and locked in a successive cooling event during the Early-Middle Ordovician.