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Soil quality assessment serves as an index for appraising soil sustainability under varied soil management approaches. Our current investigation was oriented to establish a minimum data set (MDS) of soil quality indicators through the selection of apt scoring functions for each indicator, thus evaluating soil quality in the Himalayan foothills. The experiment was conducted during two consecutive years, viz. 2016 and 2017, and comprised of 13 treatments encompassing different combinations of chemical fertilizers, organic manure, and biofertilizers, viz. (i) the control, (ii) 20 kg P + PSB (Phosphorus solubilizing bacteria), (iii) 20 kg P + PSB + Rhizobium, (iv) 20 kg P + PSB + Rhizobium+ FYM, (v) 20 kg P + 0.5 kg Mo + PSB, (vi) 20 kg P + 0.5 kg Mo + PSB + Rhizobium, (vii) 20 kg P + 0.5 kg Mo + PSB + Rhizobium + FYM, (viii) 40 kg@ P + PSB, (ix) 40 kg P + PSB + Rhizobium, (x) 40 kg P + PSB + Rhizobium+ FYM, (xi) 40 kg P + 0.5 kg Mo + PSB, (xii) 40 kg P + 0.5 kg Mo + PSB + Rhizobium, and (xiii) 40 kg P + 0.5 kg Mo + PSB + Rhizobium + FYM. Evaluating the physical, chemical, and biological indicators, the integrated module of organic and inorganic fertilization reflected a significant improvement in soil characteristics such as the water holding capacity, available nitrogen, phosphorus, potassium, and molybdenum, different carbon fractions and soil biological characteristics encircling microbial biomass carbon (MBC), and total bacterial and fungal count. A principal component analysis (PCA) was executed for the reduction of multidimensional data ensued by scoring through the transformation of selected indicators. The soil quality index (SQI) established for different treatments exhibited a variation of 0.105 to 0.398, while the magnitude of share pertaining to key soil quality indicators for influencing soil quality index encircled the water holding capacity (WHC), the dehydrogenase activity (DHA), the total bacteria count, and the available P. The treatments that received an integrated nutrient package exhibited a higher SQI (T10—0.398; T13—0.372; T7—0.307) in comparison to the control treatment (T1—0.105). An enhanced soil quality index put forth for all organic treatments reflected an edge of any conjunctive package of reduced synthetic fertilizers with prime involvement of organic fertilizers over the sole application of inorganic fertilizers.