The regulatory effects of initial soil C and structure on the partitioning of new C are not well understood. An experimental foundation is needed for improved models of physical protection that include initial soil C and structural parameters. A factorial experiment (2 soils, 2 residue input levels, 3 structural disruption levels and 3 destructive sampling times) was designed to quantify the regulatory effects of initial soil C and structure on aggregate and C dynamics. Both soils had comparable texture (sandy loam) and mineralogy (kaolinitic) but widely varying C content (5 vs. 25 mg/g) and structure (20 vs. 60 % water stable macroggregation) as a result of long-term no-till (NT) and conventional till (CT) management. Structural disruption treatments ranged from passage through a sieve with 2 mm openings to 3 hours of shaking with marbles. Air dried soil (25 g) was mixed with 1-2 mm pieces of cereal rye residue (0 and 0.5 g), brought to 60% water filled pore space and incubated at 25 C. The soils were destructively sampled at 0, 1 and 8 weeks. Each sample was separated into 7 size/stability fractions and each fraction was analyzed for permanganate oxidizable and total C. The greatest increases in both macroaggregate stabilization and occlusion of C occurred in NT soils receiving residue and the highest level of structural disruption. Carbon dioxide evolution was greatest from NT soils receiving residue and the lowest level of structural disruption. Most of the positive effects of residue addition occurred within 1 week in soils with the highest levels of structural disruption. The positive effects of structural disruption on subsequent aggregate stabilization and C occlusion observed in this study suggest that slow aggregate turnover may constrain physical protection of new C in some soils.