Excess N fertilization to achieve high crop yield is a grand old practice in developing countries. However, inorganic nutrient sources considerably replenish soil organic C (SOC). In the present study, we applied six different levels of N keeping P and K constant for maize, grown under maize (Zea mays) – dhaincha (Sesbania aculeata) cropping sequence. We recorded high crop yield, profuse root biomass and SOC stock with increasing N fertilization. Moreover, water holding capacity, microbial biomass carbon and particulate organic carbon improved significantly with increasing levels of N. Conversely, bulk density, mineral associated organic carbon and pH decreased with increasing application of inorganic N. Furthermore, a significant positive correlation was recorded between root biomass and soil organic carbon. A study of the sensitivity index showed particulate organic carbon and microbial biomass carbon to be good indicators of nutrient management practices. Dhaincha cultivation accelerated C and N mineralization in soil, which is reflected in increased biomass and crop yield. Hence, we conclude that inorganic N fertilization rate (72-80 kg ha^-1) in maize-dhaincha cropping sequence successfully maintains the SOC balance and optimize N stock in soil.