The long-term effect of partially substituting chemical fertilizers by organic inputs on soil quality and yield of pearl-millet and wheat under semi-arid region of Indo-Gangetic plains of India is unclear. This decadal field experiment (2009-2019) evaluated the impact of partial substitution of chemical fertilizers through organic inputs on soil carbon, microbial dynamics, soil quality and yield of pearl millet-wheat system. The experiment was laid out under randomized block design (RBD) with seven treatments and three replications in ten consecutive cropping cycles from 2009 to 2019. The seven treatments were: Ck- no chemical fertilizer, FYM-farm yard manure @15 Mg ha(-1), RDF- recommended dose of N and P, STCR-I- chemical fertilizer for achieving 3.0 and 5.5 Mg ha(-1) targeted yield of pearl millet and wheat, respectively, STCR-II- chemical fertilizer for achieving 3.5 and 6.0 Mg ha(-1) targeted yield of pearl millet and wheat, respectively, IPNS-I- FYM + chemical fertilizer for achieving 3.0 and 5.5 Mg ha(-1) targeted yield of pearl millet and wheat, respectively and IPNS-II-FYM + chemical fertilizer for achieving 3.5 and 6.0 Mg ha(-1) targeted yield of pearl millet and wheat, respectively. Treatment IPNS-I and IPNS-II improved nutrient supply system, and yields of pearl millet and wheat by lowering soil pH (7.78 and 7.79), soil bulk density (1.38 Mg m(3)) and enhancing soil organic carbon (0.83 and 0.85%), C-stock (17.1 and 17.6 Mg C ha(-1)) and its buildup rate (1.71 to 1.76 Mg C ha(-1) yr(-1)). Treatments FYM, IPNS-I and IPNS-II significantly (P < 0.05) enhanced microbial biomass carbon, potential activities of soil enzymes, soil nutrients and soil quality over the STCR-II, STCR-I, RDF and Ck, however, microbial (M-q) and metabolic quotient exhibited reverse trends. The highest SQI (0.795) was recorded with IPNS-I followed by IPNS-II (0.791), T-2 (0.771) and the lowest in Ck (0.341). Available P, acid phosphatase, available N and Mq were the key soil quality indicators in MDS for the pearl millet-wheat production in semi-arid zone, contributing 20.4, 21.0, 19.6 and 7.96% toward soil quality development, respectively. Treatment IPNS-I and IPNS-II not only achieved the targeted yield of pearl millet and wheat within +/- 10% yield deviation, but also increased pearl millet yields by 7.83 and 25.6%, and wheat yield by 10.4 and 23.9% over RDF, respectively due to improving SQI. As a result, SQI had significant correlation with grain and stover/straw yield of pearl millet and wheat indicated prominent influence of partial substitution of organic manure to inorganic fertilizers. Thus, our results evinced that long-term partial substitution of inorganic fertilizer based on targeted yield approach of soil test crop response (STCR) provides better environment for pearl millet-wheat productivity in semi-arid Inceptisol of India.