For nutrient management in a cropping system, one needs to know the residual effect of organics on the succeeding crops. The work was carried out for better understanding the impact of different organic manures on the popcorn-potato cropping system which is common in many regions of India. To assess the effect of recommended N rates applied as inorganic fertilizers (IF), farmyard manure (FYM), leaf compost (LC) and vermicompost (VC) on soil health and productivity in popcorn-potato cropping system, field experiments were conducted for two consecutive years. Application of IF significantly improved crop growth and yield in popcorn but had a detrimental effect on soil health. Whole N (120 kg N ha−1) applied through FYM boosted growth and yield leading to 48.3% and 15.6% higher system productivity over control and inorganic N application, respectively. FYM equivalent to 120 kg N ha−1also significantly improved the soil fertility in terms of residual available soil N, P and K, soil organic carbon (SOC) and soil carbon stocks in popcorn-potato system. Further, the application of organic manures, particularly FYM (equivalent to 120 kg N ha−1) increased SOC over initial values by 23.8% and 35.8% during 2008–09 and 2009–10, respectively. A multiple correlation analysis (RSY.NPKSOC = 0.87; p < 0.001) showed that SOC and available forms of N, P and K significantly influenced the system yield. Regression analysis clearly indicated that system productivity was positively correlated with available soil nutrients. The application of organic manure also improved microbial populations (bacteria, fungi and actinomycetes), soil microbial carbon biomass (SMCB), dehydrogenase activity and soil bulk density (BD). The latter effect was not observed when inorganic fertilizers were applied. A FYM application rate equivalent to 120 kg N ha−1 to popcorn and 60 kg N ha−1 to potato resulted in maximum system productivity and profitability in terms of highest gross and net returns and cost:benefit ratio. The beneficial effect of applying organic manures in the cropping system was due to the improvement of soil health by addition of organic manure and easy supply of other plant nutrients.