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The results from the long-term fertilizer experiment on soybean-wheat system indicated that the all of the N fractions were increased in both the surface and sub surface soil layers with the continuous application of fertilizer N and FYM. The balance use of nutrients (100% NPK) and its integrated application with FYM (100% NPK+FYM) improved the N content and its fractions in soil. However, the continuous cropping without fertilization and/or imbalance use of nutrients (100% N alone) proved deleterious to soil health as it resulted in a marked depletion of various N fractions in both surface and sub-surface soils. Hence, the conjoint application of inorganic fertilizers with organic manure could be the better option for long-term sustaining crop productivity and soil fertility in a Vertisol under soybean-wheat cropping system.