Soybean is very energy-rich crop containing 40–45% protein and 20–22% oil. It has already emerged as one of the promising oilseed crops in India. Soybean is grown in different soil types and considered as moderately nutrient exhaustive crop. Effective nutrient management practices are essential for modern soybean varieties for achieving higher productivity and maintenance of soil health. It is also recognized that integrated use of chemical fertilizers, organic manures and biofertilizers is a suitable proposition for not only sustaining the productivity of 2.0 t ha−1 but also for improvement in soil health in a long run. Among the three primary nutrients, viz. N, P and K, the deficiency of K generally occurs under field conditions. Being an oilseed crop, the requirement for sulfur is high, the deficiency of S is also observed, where the source of P fertilizer is diammonium phosphate (DAP). Among the micronutrients, B deficiency is observed on sandy soils in soybean growing areas. From the ongoing long-term fertilizer experiment with soybean as test crop for five decades, the results revealed that application of NPK through chemical fertilizers can produce mean seed yield of 1574 kg ha−1. Further application of lime or Farm Yard Manure (FYM) along with recommended dose of NPK increased the seed yield of soybean by 18–23% as compared to the optimal dose of fertilizers over the years. Growing of soybean over the years improved soil health by supplying biomass, increasing organic carbon and micronutrients and improving physical and biological health of soil.