The Neoproterozoic carbonate rocks of the Araras Group (Amazon Craton) and the Sete‐Lagoas and Salitre Formations (São Francisco Craton) share a statistically indistinguishable single‐polarity (reversed) characteristic direction. This direction is associated with paleomagnetic poles that do not align with the expected directions for primary detrital remanence. We employ a combination of classical rock magnetic properties and micro imaging/chemical analysis (in thin sections) using synchrotron radiation to examine these remagnetized carbonate rocks. Magnetic data indicate that most samples lack the anomalous hysteresis properties typically associated with carbonate remagnetization (except for distorted loops). Through a combination of Scanning Electron Microscopy with Energy Dispersive X‐ray Spectroscopy (SEM‐EDS), X‐ray Fluorescence (XRF), and X‐ray Absorption Spectroscopy (XAS), we identified 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 do most of the iron sulfides, and are spatially associated with potassium‐bearing aluminosilicates. While fluid percolation and organic matter maturation play a role, smectite‐illitization appears to be crucial for the growth of these phases. X‐ray diffraction analysis, in addition, identifies these silicates as predominantly highly crystalline illite, suggesting exposure to epizone temperatures. These temperatures were likely reached during the final stages of the Gondwana assembly (Cambrian), but remanence was only locked in afterward, in successive cooling events during the Early Middle Ordovician. This is supported by the carbonates' paleomagnetic pole positions compared to Gondwana's apparent polar wander path, and the absence of reversals, contrasting with the high reversal frequency of the Late Ediacaran/Cambrian.