Purpose Protective mineral-organic associations are the quantitatively most important soil carbon storage mechanism, but their vulnerability to environmental change is largely uncertain. While it is well established that root growth can promote (or “prime”) the microbial decomposition of organic matter (OM), our mechanistic knowledge of the ability of roots to destabilize OM protected within mineral-organic associations remains limited. Here we examined how the composition of root-derived compounds (rhizodeposits) affects the stability of mineral-organic associations. Methods In model systems, we tested the ability of functionally distinct low-molecular weight compounds (ligands, reductants, simple sugars) commonly observed in the rhizosphere to cause the mobilization and mineralization of isotopically labeled OM from different mineral types (Fe and Al hydroxides). Results Our results showed that all compounds stimulated mobilization and mineralization of previously mineral-associated OM. However, OM bound to Al hydroxide was less susceptible to mobilization than OM bound to Fe hydroxide. In batch solution without soil, the strong ligand oxalic acid mobilized more mineral-associated OM than the reducing agent catechol or the simple sugar glucose. This finding was in line with our initial hypotheses. In model soil, however, glucose (sugar) and catechol (reductant) revealed a greater mobilization potential than oxalic acid (ligand) for both mineral types, suggesting that OM mobilization in soils may be microbially mediated, rather than driven by direct mineral dissolution. Conclusion Together, our results suggest a strong mechanistic linkage between the composition and functionality of rhizodeposits and their ability to destabilize mineral-associated OM.