Physicochemical binding in organo-mineral complexes of soil micro-aggregates contributes to carbon stabilization in soils. We combined nano-scale sample processing with synchrotron based scanning transmission x-ray microscopy and near edge x-ray absorption fine structure spectroscopy to investigate the protection of carbon within interior and exterior pore regions of intact soil micro-aggregate sections. We observed a highly patchy, near random nano-scale distribution of C that was stabilized between pore spaces and bound to the mineral domain. Organo-mineral formations of nano-aggregates were visible proximal to mineral and organic matter assemblages. Our results indicate that combining STMX with C NEXAFS affords a powerful, non-destructive approach to identify and fingerprint complex structural characteristics of organic macromolecules that stabilize C in soil