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This study introduced CA to manage agro-ecosystems for improved and sustained productivity, and increased farmers’ profits while maintaining natural resources in rice-wheat systems of the IndoGangetic Plains of India. The project managed natural resources at the farm, village, and landscape scales to increase synergies between food production and ecosystem conservation. The results show that the CA-based rice-wheat (RW) system integrated with mungbean improved the system productivity by ∼10%, profitability by 20–30% using 15–30% less irrigation water, and 20–25% less energy input compared to conventional RW system in the IGP. Replacing rice with maize improved the productivity by 10-15% and profitability by 40–50% using ∼70% less irrigation water. CA layered with subsurface drip irrigation (SDI) in CA-based rice/maize systems recorded ∼5% higher system productivity and saved ∼50% of irrigation water compared to flood irrigation in CT-based systems. CA-based systems are found more adapted to extreme climatic conditions and can mitigate the negative effects of climatic stresses like terminal heat and water stress.