Improved management of agricultural soils has potential for sequestering carbon (C) and reducing the accumulation of atmospheric carbon dioxide. Development of management practices to increase C sequestration is dependent on improved understanding of soil processes influencing long-term storage of C. A field study was conducted to compare surface C source quality and above- vs. below-ground addition of annual or perennial plant biomass effects on particulate organic matter (POM), total labile C (TLC), and total organic C (TOC). Since microaggregate stabilization within macroaggregates is the main mechanism for sequestering C, aggregate size distribution, expressed as mean weight diameter (MWD), and wet aggregate stability (WAS) was also measured. After 5 years POM decreased in plots receiving surface application of readily available substrate (sucrose and alfalfa pellets) and the bare surface control. Plots receiving plant additions [wood chips, growing wheat (Triticum aestivum L.) crop, growing switchgrass (Panicum virgatum L.) crop and fallow receiving either wheat or switchgrass residue] exhibited higher TLC and TOC content. Plots receiving plant residue maintained MWD and those supporting live plants exhibited increasing WAS. Surface plant residue protected the soil against raindrop impact and reduced the intensity of wetting and drying cycles allowing the development of larger more stable aggregates resulting in C accrual.