Soil aggregates play an important role in the stabilization of soil organic matter. The intimate associations of decomposing organic matter with soil minerals in aggregates may enable more residues to enter into protected organomineral associations with longer residence times. We used increasing disruptive energy to physically fractionate particulate- and mineral-associated organic matter according to the hierarchical organization of soil aggregate structure (within microaggregates, within macroaggregates but outside microaggregates, and unaggregated). In addition, silt- and clay-sized mineral-associated fractions from each location were acid hydrolyzed to isolate chemically resistant carbon from more labile carbon. We evaluated the role that aggregate hierarchy plays in the storage and turnover of carbon by using the natural abundance of stable carbon isotopes following a switch from C4 to C3 grassland on a silt loam in Kansas, USA. Sixty-two years after the switch, soil carbon stocks had changed only slightly, and most fractions showed little or no difference in carbon content between the two sites, providing near-equilibrium conditions. About 55-60% of particulate organic matter was macroaggregate-protected but located outside microaggregates, and all particulate organic matter was essentially C3-derived. However, both the amounts and residence times of carbon in silt- and clay-sized fractions differed depending on location within the soil's aggregate hierarchy. Microaggregates afforded greater protection for old C4-derived mineral-associated carbon than other locations, and acid-resistant silt- and clay-associated carbon in microaggregates exhibited the longest residence times. However, new mineral-associated carbon also accumulated more within microaggregates, demonstrating that acid resistant silt- and clay-associated carbon pools in microaggregates contain both very stable and relatively young organic matter. Thus, microaggregates appear to contribute to both the protection of old mineral-associated carbon and the creation of new organomineral associations, suggesting that the stabilization of mineral-associated carbon results from an interaction between physical and chemical protection mechanisms.