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This paper used a long-term field experiment to better understand the role of deteriorating soil health, stagnation of yield in rice-wheat systems in the Indo-Gangetic Plains and environmental pollution. Four crop scenarios with conservation agriculture (CA), crop intensification and diversified cropping as intervening technology aimed to evaluate the sustainability of the systems. Among the 4 scenarios, the S3 scenario (a legume crop was taken along with rice and wheat with full CA) had greater amount of total soil organic carbon, passive pool of carbon and higher system rice equivalent yield, thus, is considered the best cropping management practice to maintain soil health and food security in the middle IGP.