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The ever shrinking agricultural land availability and the swelling demand of food for the growing population fetch our attention towards utilizing partially reclaimed sodic soils for cultivation. In the present investigation, we compared six treatments, like control (T1), existing farmers’ practice (T2), balanced inorganic fertilization (T3) and combined application of green gram (Vigna radiate) with inorganic NPK (T4), green manure (Sesbania aculeate) with inorganic NPK (T5), and farmyard manure with inorganic NPK (T6), to study the influence of nutrient management on soil organic carbon sequestration and soil fertility under long-term rice-wheat cropping system along with its productivity in gypsum-amended partially reclaimed sodic soils of semi-arid sub-tropical Indian climate. On an average, combined application of organics along with fertilizer NPK (T4, T5, and T6) decreased soil pH, ESP, and BD by 3.5, 13.0, and 6.7% than FP (T2) and 3.7, 12.5, and 6.7%, than balanced inorganic fertilizer application (T3), respectively, in surface (0-20 cm). These treatments (T4, T5, and T6) also increased 14.1% N and 19.5% P availability in soil over the usual farmers’ practice (FP) with an additional saving of 44.4 and 27.3% fertilizer N and P, respectively. Long-term (6 years) incorporation of organics (T4, T5, and T6) sequestered 1.5 and 2.0 times higher soil organic carbon as compared to the balanced inorganic (T3) and FP (T2) treatments, respectively. The allocation of soil organic carbon into active and passive pools determines its relative susceptibility towards oxidation. The lower active to passive ratio (1.63) in FYM-treated plots along with its potentiality of higher soil organic carbon (SOC) sequestration compared to the initial stock proved its acceptability for long-term sustenance under intensive cropping even in partially reclaimed sodic soils. Among all the treatments, T4 yielded the maximumfrom second year onwards. Moreover, after 6 years of continuous cultivation, the observed EWY (2011-2012) was found to be 41.9 and 33.1% higher in T4 as compared to FP (T2) and T3, respectively. Thus, for maintaining higher yield coupled with improved SOC sequestration and nutrient availability, T4 followed by T6 treatments would be the suitable options for long-term intensive rice-wheat system in partially reclaimed sodic soils of northern India.