Cover crops (CCs) offer ecosystem benefits, yet their impact on subsequent crop yields varies with climate, soil, and management practices. Using the Decision Support System for Agrotechnology Transfer (DSSAT) at the University of Nebraska-Lincoln’s Eastern Nebraska Research, Education, and Extension Center (ENREEC), we identified optimal cereal rye management strategies focusing on planting, termination, and the intervals between CC termination and corn planting. Results showed minimal impact of CC management variations on corn yield, underscoring corn’s resilience to management changes. Delayed planting notably decreased CC biomass, nitrogen uptake, and biomass nitrogen content on average by 8.8%, 11%, and 9.2% for every five-day delay from 25 September. Every 5-day increase in the interval between CC termination and corn planting reduced biomass by 19.3%. Conversely, each 5-day delay in CC termination from 10 September to 10 October increased biomass by 30%, enhancing SOC accumulation. SOC changes over the 30-year simulation ranged from 5.8% to 7.7%, peaking with late May terminations. The earliest termination showed the highest nitrogen content in biomass (3.4%), with the lowest (0.69%) in mid-May. Our results demonstrate that strategic CC management supports soil health without negatively impacting corn yield in Eastern Nebraska, providing valuable insights for farmers and practitioners aiming to implement sustainable CC practices while preserving crop productivity.