Increased input efficiency is one of the main challenges for a modern agricultural enterprise. One way to optimize production cycles is to rationalize crop residue utilization. In conditions where there is limited use of mineral fertilizers and without applying manure, plant residues may be used as an organic fertilizer as a way to maintain carbon sustainability. A systems approach to manage after-harvest nitrogen fertilizers allowed for the maintenance of a proper nitrogen/carbon ratio while accounting for spatially variable biomass production. Variable rate technology provided a significant reduction in the use of nitrogen fertilizer. Two years of experimentation with corn grown after a winter wheat crop rotation, demonstrated a number of soil improvements (e.g., amount of carbon dioxide, biological activities, aeration), which lead to generally higher and more stable yields.