AbstractThe extent to which cover crops (CCs) accumulate soil organic carbon (SOC) in the entire soil profile is still unclear. We measured SOC, permanganate oxidizable C (POX‐C), and particulate organic matter (POM) concentrations down to 60‐cm soil depth in early [2–3 week before corn (Zea mays L.) planting]‐ and late‐terminated (at corn planting) winter rye (Secale cereale L.) CCs in rainfed and irrigated no‐till continuous corn systems in the U.S. Corn Belt after 10 years. CCs increased SOC stock and SOC, POX‐C, and POM concentrations but only in the irrigated system in the upper 5‐cm depth. Late‐terminated CC increased SOC concentration by 4.710 ± 3.501 g kg−1 and accumulated SOC at 0.207 ± 0.145 Mg C ha−1 year−1. It increased POX‐C and POM concentrations, on average, by 1.194 times. CCs likely increased SOC in the irrigated system by producing more biomass (2.247 ± 0.370 Mg ha−1) than in the rainfed system (0.949 ± 0.338 Mg ha−1). At least 2 Mg ha−1 of CC biomass may be needed to increase SOC. Because winter CCs often produce <1 Mg ha−1 of biomass when typically planted late and terminated early, extending the CC growing window by terminating CCs at or after crop planting (planting green) may boost CC biomass and SOC accumulation, although high‐C soils or Mollisols, such as our study soils (>22 g C kg−1), may limit SOC gains. We submit CCs would sequester more SOC in low‐C, eroded, and low‐fertility soils. Overall, winter rye CCs minimally alter soil C in the soil profile in no‐till continuous corn systems after 10 years.