Specific impacts of organic management practices on soil organic matter characteristics have not been documented. This study tested how organic management practices influence soil fertility by investigating whether 10 yr of organic or conventional management generated differences in biologically active soil organic matter (SOM) pools at the Rodale Institute Research Center’s long-term Farming Systems Trial experiment (FST). The experiment included an organically managed rotation that was animal based, an organic treatment that was cash-grain based, and a conventional cash-grain-based rotation. The biologically active SOM matter pools of the three FST treatment soils were compared through characterization of soil CO2 evolution, available inorganic N pools and N mineralization rates, water-dispersible organic carbon (WDOC), and participate organic matter (light fraction). Soils receiving the organic treatments accumulated biologically active C. Accumulated organic matter in the manure-amended soil was the most labile whereas the cover-cropped soil accumulated the most organic matter overall. In the cover-cropped soil, higher total C and N, participate SOM, and reduced WDOC contents indicated that its SOM was more stable than SOM in the other two treatment soils. The conventionally managed soil had the lowest biological activity (N supply and soil respiration rates) and did not accumulate SOM during the 10-yr experiment. Assays that characterize particulate organic matter emerged as the best indices of biologically active SOM because they documented important quality (i.e., biological lability) and quantity aspects of SOM character in the Rodale FST soils.