Addressing sustainability within food systems is challenging due to their multifaceted nature. Here, we evaluate crop-restructuring pathways for Indian agricultural system by integrating nutrient, water, greenhouse gas, economic, and interstate trade-network accounting. We show that the nitrogen-focused crop restructuring strategy reduces nitrogen surplus by 13.4% and water use by 18.6%. This approach maintains baseline calorie production, narrows the benchmarked cereal net-return deficit, and mitigates greenhouse gas emissions by 8.7%. Relative to water-focused restructuring, the nitrogen-focused strategy delivers larger reciprocal co-benefits by about 4.6-fold, resulting in a decrease in socio-environmental costs associated with nitrogen pollution of around $1.19 billion USD. The resulting agricultural restructuring substantially expands alternative-cereal trade in the interstate trade network. Overall, our analysis shows that integrating nutrient management into crop-restructuring strategies can support food-system sustainability in India and other resource-constrained agricultural systems.