Soil organic carbon (SOC) storage is a critical component of the overall sustainability of bioenergy cropping systems. Predicting the influence of cropping systems on SOC under diverse scenarios requires a mechanistic understanding of the underlying processes driving SOC accumulation and loss. We used a density fractionation technique to isolate three SOC fractions that are conceptualized to vary in SOC protection from decomposition. The free light fraction (FLF) is particulate SOC that is present in the inter-aggregate soil matrix, the occluded light fraction (OLF) is contained within aggregates, and the heavy fraction (HF) is associated with minerals. We evaluated surface (0 to 10 cm depth) SOC fraction changes from baseline conditions 5 years after biofuel cropping system establishment at two temperate sites with contrasting soil textures. The biofuel cropping systems included no-till maize, switchgrass, prairie, and hybrid poplar. The FLF concentration (g fraction C g bulk soil-1) did not change significantly from baseline levels under any of the cropping systems at either site after 5 years. Except for poplar, OLF concentrations were reduced in all systems at the site with coarse-textured soils and maintained at the site with fine-textured soils. In poplar systems, OLF concentrations were maintained on coarse-textured soils and increased on fine-textured soils. The HF concentrations also increased under poplar on the coarse-textured soil. A structural equation model indicated that OLF concentrations increased with lower litter C:N, and HF concentrations increased with greater litter quantity and lower litter C:N mass ratios. C:N increased over time within all SOC fractions, suggesting that all pools are sensitive to land-use change on sub-decadal timescales. In agreement with modern SOC theory, our empirical results indicate that increasing litter input quantity and promoting plant species with low C:N litter may improve SOC storage in aggregate and mineral-associated soil fractions.