Organo-mineral interactions control the stabilisation of soil organic matter (SOM) in mineral soils. Biochar can enhance these interactions via a range of mechanisms including Al-dominant cation bridging in acidic soils, ligand exchange, H-bonding, and π- π-bonding with polycyclic aromatics. But, field-based evidence of their magnitude is lacking. Here we assessed the role of organo-mineral interactions on the observed biochar-induced negative priming of native soil organic carbon (SOC) in a Ferralsol under annual ryegrass. Using repeated pulse labelling, the magnitude of production and fate of recently photosynthesised 13C was traced amongst: soil plus root respiration, root biomass, soil aggregates and aggregate-associated C fractions. Biochar (Eucalyptus saligna, 450 °C) amendment (30 Mg ha−1) increased total belowground 13C recovery by 10% compared to the unamended control over the 12 month sampling period. We detected the greatest quantity of rhizodeposit in the mineral-protected SOM within macroaggregates (250–2000 μm). Through synchrotron-based spectroscopic analysis of bulk soils, we provide evidence of a mechanism for biochar-induced negative priming which is the accumulation of rhizodeposits in organo-mineral (i.e. aggregate-protected and silt/clay-bound) fractions.