Soil salinity is a major environment stress impairing crop production and accelerating soil degradation. Use of soil amendments are practical solutions for altering soil quality to enhance crop productivity in these soils. Hence, we systematically evaluated the impact of soil amendments practices on crop productivity, nutrient use efficiency, soil properties, soil quality index, economics and energetics on soybean-mustard cropping system in sodic Vertisol. In this study, eight treatments comprising of various combinations of soil amendments such as gypsum (@2.5 t ha−1), farmyard manure (FYM@10 t ha−1), crop residue (CR@1.5 t ha−1 of soybean residue during rabi and 3 t ha−1 of mustard residue during kharif season) with recommended fertilizer doses (RNPK) was evaluated in randomized block design with three replications for four consecutive years in soybean-mustard cropping sequences (2016–2019). Results demonstrated that application of gypsum with CR and FYM recorded a significant drop in exchangeable sodium percentage (ESP) (45–48 %), and bulk density (BD) (3–6 %) than that of control. Organic amendment in conjunction with gypsum and chemical fertilizer significantly improved soil chemical, physical and biological properties than that under control and inorganic fertilizer alone treatments. Based on principal component analysis and correlation matrix, minimum data set identified ESP, pH, BD, organic carbon, available nutrients, biomass carbon, calcium content, dehydrogenase as the most important properties controlling soil quality. Integration of RNPK+Gypsum+CR and RNPK+Gypsum+FYM are found superior leading to higher crop yield in soybean (1.23 and 1.21 Mg ha−1 respectively), mustard (1.43 and 1.39 Mg ha−1 respectively), better nutrient recovery efficiency (77 and 53 % respectively), improved soil quality index (0.90 and 0.93 respectively), and higher economic return (benefit: cost ratio-2.88 and 2.1 respectively).Therefore, this study findings highlighted the conjunctive use of gypsum with organic amendments is effective in reclaiming salt stress, improving soil health and crop productivity under oilseed cropping sequence in degraded soils of semi-arid tropics.