Over years of intensive cultivation and imbalanced fertilizer use, the soils of the Indiansubcontinent 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 managesoil health. However, owing to the steadily increasing demands for food by the overgrowingpopulations 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 thisregion have already recognized this problem and have modified farming systems towardintegrated nutrient management (INM) practices. The INM concept aims to design farmingsystems to ensure sustainability by improving soil health, while securing food for the populationby improving crop productivity. Therefore, this paper was synthesized to quantify the impact androle of INM in improving crop productivity and sustainability of the RWCS in the context of theIndian 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 grainyield of both crops with the use of INM over inorganic fertilizers only (IORA), organic fertilizersonly (ORA), and control (no fertilizers; CO) treatments. The increase in grain yield was significantat p < 0.05 for rice in INM over ORA and CO treatments. For wheat, the increase in grain yield wassignificant at p < 0.05 in INM over IORA, ORA, and CO treatments. The yield differences in theINM treatment over IORA were 0.05 and 0.13 Mg ha−1, respectively, in rice and wheat crops. Thepercent yield increases in INM treatment over IORA, ORA, and CO treatments were 2.52, 29.2, and90.9, respectively, in loamy soil and 0.60, 24.9, and 93.7, respectively, in clayey soil. The net returnsincreased by 121% (INM vs. CO) in rice, and 9.34% (INM vs. IORA) and 127% (INM vs. CO) inwheat crop. Use of integrated nutrient management had a positive effect on soil properties ascompared to other nutrient management options. Overall, the yield gain and maintenance of soilhealth due to INM practices over other nutrient management practices in RWCS can be a viablenutrient management option in the Indian subcontinent.