Accurate quantification of soil organic carbon (OC) and nitrogen (N) concentrations are necessary to ascertain the effects of land use, crop rotation systems, and management practices on soil C and N sequestration potential. Soil OC and total N were determined by various methods in a Typic Albaqualf under native tallgrass prairie and agricultural soil cropped to a rice (Otyza sativa L.)-soybean (Glycine max L.)-wheat (Triticum aestivum L.)/soybean rotation that has been annually cultivated for 15, 26, and 44 years. Two wet-oxidation, methods, the Walkley-Black (WB) and modified Walkley-Black (mod WB), and high-temperature combustion using a Carlo-Erba and LECO analyzer were used to determine the effects of assessment method on soil OC concentration, while the high-temperature combustion method using the Carlo-Erba and LECO analyzer were used to determine the effects of assessment method on total soil N concentration. Soil OC and total N concentrations determined by high-temperature dry combustion using the Carlo-Erba and LECO analyzers did not differ significantly. Soil OC concentrations determined by the modWB method were generally significantly higher than those from the WB or high-temperature combustion methods. Despite significant linear correlation (r > 0.74; p < 0.001) between soil OC concentrations by wet-oxidation and dry-combustion methods, assessment methodology significantly affected interpretations regarding changes in soil OC storage over time. The results of this study indicate that the choice of assessment methodology is a critical decision for the accurate quantification of soil OC concentration, content, and change over time.