Long-term field experiments are among the best means to predict soil management impacts on soil carbon storage. Soil organic carbon (SOC) and natural abundance 13C ([delta]13C) were sensitive to tillage, stover harvest, and nitrogen (N) management during 13 years of continuous corn (Zea mays L.), grown on a Haplic Chernozem soil in Minnesota. Contents of SOC in the 0-15 cm layer in the annually-tilled [moldboard (MB) and chisel (CH)] plots decreased slightly with years of corn after a low input mixture of alfalfa (Medicago sativum L.) and oat (Avena sativa L.) for pasture; stover harvest had no effect. Storage of SOC in no-till (NT) plots with stover harvested remained nearly unchanged at 55 Mg ha-1 with time, while that with stover returned increased about 14%. The measured [delta]13C increased steadily with years of corn cropping in all treatments; the NT with stover return had the highest increase. The N fertilization effects on SOC and [delta]13C were most evident when stover was returned to NT plots. In the 15-30 cm depth, SOC storage decreased and [delta]13C values increased with years of corn cropping under NT, especially when stover was harvested. There was no consistent temporal trend in SOC storage and [delta]13C values in the 15-30 cm depth when plots received annual MB or CH tillage. The amount of available corn residue that was retained in SOC storage was influenced by all three management factors. Corn-derived SOC in the 0-15 cm and the 15-30 cm layers of the NT system combined was largest with 200 kg N ha-1 and no stover harvest. The MB and CH tillage systems did not influence soil storage of corn-derived SOC in either the 0-15 or 15-30 cm layers. The corn-derived SOC as a fraction of SOC after 13 years fell into three ranges: 0.05 for the NT with stover harvested, 0.15 for the NT with no stover harvest, and 0.09-0.10 for treatments with annual tillage; N rate had no effect on this fraction. Corn-derived SOC expressed as a fraction of C returned was positively biased when C returned in the roots was estimated from recovery of root biomass. The half-life for decomposition of the original or relic SOC was longer when stover was returned, shortened when stover was harvested and N applied, and sharply lengthened when stover was not harvested and N was partially mixed with the stover. Separating SOC storage into relic and current crop sources has significantly improved our understanding of the main and interacting effects of tillage, crop residue, and N fertilization for managing SOC accumulation in soil.