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Over years of intensive cultivation and imbalanced fertilizer use, the soils of the Indian subcontinent have become deficient in several nutrients and are impoverished in organic matter. Recently, this region has started emphasizing a shift from inorganic to organic farming to manage soil health. However, owing to the steadily increasing demands for food by the overgrowing populations of this region, a complete shift to an organic farming system is not possible. The rice–wheat cropping system (RWCS) is in crisis because of falling or static yields. The nations of this region have already recognized this problem and have modified farming systems toward integrated nutrient management (INM) practices. The INM concept aims to design farming systems to ensure sustainability by improving soil health, while securing food for the population by improving crop productivity. Therefore, this paper was synthesized to quantify the impact and role of INM in improving crop productivity and sustainability of the RWCS in the context of the Indian subcontinent through meta-analysis using 338 paired data during the period of 1989–2016. The meta-analysis of the whole data for rice and wheat showed a positive increase in the grain yield of both crops with the use of INM over inorganic fertilizers only (IORA), organic fertilizers only (ORA), and control (no fertilizers; CO) treatments. The increase in grain yield was significant at p < 0.05 for rice in INM over ORA and CO treatments. For wheat, the increase in grain yield was significant at p < 0.05 in INM over IORA, ORA, and CO treatments. The yield differences in the INM treatment over IORA were 0.05 and 0.13 Mg ha−1, respectively, in rice and wheat crops. The percent yield increases in INM treatment over IORA, ORA, and CO treatments were 2.52, 29.2, and 90.9, respectively, in loamy soil and 0.60, 24.9, and 93.7, respectively, in clayey soil. The net returns increased by 121% (INM vs. CO) in rice, and 9.34% (INM vs. IORA) and 127% (INM vs. CO) in wheat crop. Use of integrated nutrient management had a positive effect on soil properties as compared to other nutrient management options. Overall, the yield gain and maintenance of soil health due to INM practices over other nutrient management practices in RWCS can be a viable nutrient management option in the Indian subcontinent. [ABSTRACT FROM AUTHOR]