The loss of organic matter (OM) from soil during long-term agricultural cropping results in a decrease in the inherent fertility of the soil as well as releasing greenhouse gases. Despite the importance of organo-mineral associations in the stabilization of OM within soils, much remains unknown about these organo-mineral associations. We used nano-scale secondary ion mass spectrometry (NanoSIMS) to investigate the incorporation and stabilization of ¹³C and ¹⁵N labelled residues of lucerne (Medicago sativa) and buffel grass (Cenchrus ciliaris) when incubated in a Vertisol from temperate Australia for up to 365 d. We show that newly-added OM forms organo-mineral associations through two mechanisms. Firstly, it was observed that the newly-added OM forms associations with the existing mineral-bound OM. However, this apparent stabilization of newly-added OM by associating with existing mineral-bound OM was not influenced by the C:N ratio of the plant residues, with the lucerne residues (C:N ratio of 11) being incorporated to a similar extent as the buffel grass (C:N ratio of 35). Secondly, we observed that N-rich microbial metabolites attached directly to mineral particle surfaces that did not contain existing OM patches, thereby creating new organo-mineral associations through which additional stabilization of OM would be possible. The information obtained in this study is valuable in understanding the stabilization of OM through organo-mineral associations, and raises the possibility of using cover crops or catch crops with narrow C:N ratios to allow for formation of new organo-mineral associations for increased stabilization of OM in soil.