One of our current challenges is to quantify the mechanisms, capacity, and longevity of C stabilization in agricultural lands. The objectives of this study were to evaluate the long-term (10 yr) role of C input in soil organic carbon (SOC) sequestration and to identify underlying mechanisms of C stabilization in soils. Carbon input and SOC sequestration, as governed by crop management strategies, were assessed across 10 Mediterranean cropping systems. Empirically derived relationships between yield and aboveground plus belowground crop biomass as well as estimates of C contributions from crop residues and manure amendments were used to quantify cumulative C inputs into each cropping system. Soil samples were separated into four aggregate size classes (>2000, 250-2000, 53-250, and <53 μm) and into three soil organic matter (SOM) fractions within the large (>2000 μm) and small (250-2000 μm) macroaggregates. Aggregate stability increased linearly with both C input (r2 = 0.75, p = 0.001) and SOC (r2 = 0.63, p = 0.006). Across the 10 cropping systems, annual soil C sequestration rates ranged from -0.35 to 0.56 Mg C ha-1 yr-1. We found a strong linear relationship (r2 = 0.70, p = 0.003) between SOC sequestration and cumulative C input, with a residue-C conversion to SOC rate of 7.6%. This linear relationship suggests that these soils have not reached an upper limit of C sequestration (i.e., not C saturated). In addition, C shifted from the <53-μm fraction in low C input systems to the large and small macroaggregates in high C input systems. A majority of the accumulation of SOC due to additional C inputs was preferentially sequestered in the microaggregates-within-small-macroaggregates (mM). Hence, the mM fraction is an ideal indicator for C sequestration potential in sustainable agroecosystems.