Context: The maize-wheat (Zea mays L.-Triticum aestivum L.) system is one of the most widely practiced production systems in South Asia, playing a critical role in regional agri-food and nutritional security. However, it is increasingly threatened by climate change, declining soil health, and diminishing water resources. Conventional intensive tillage, inefficient residue use, and blanket nutrient application have led to stagnating yields, reduced soil organic carbon, and poor resource-use efficiency, raising concerns over the long-term sustainability. Objective: This study aimed to evaluate the effects of different (i) crop establishment methods (CEMs), (ii) residue management (RM), and (iii) nutrient management (NM) strategies on productivity, profitability, energy-use efficiency, and soil health in the Maize-Wheat (M-W) system, with a focus on identifying potential trade-offs and synergies among these conservation agriculture (CA) practices. Methods: A two-year field experiment (2018-19-2019-20) was conducted at ICAR-Indian Agricultural Research Institute (28 degrees 40 ' N, 77 degrees 12 ' E; 228.6 m aMSL), New Delhi under a semi-arid climate. The trial used a split-split plot design with three replications. Treatments included: (i) two tillage systems: conventional tillage (CT) and permanent raised beds (PRB); (ii) two residue management options: residue removal (-R) and residue retention (+R at 3 Mg ha(-1)); and (iii) three nutrient strategies: soil test-based (STB), Nutrient Expert (NE), and NE integrated with GreenSeeker (NE+GS). Results: PRB increased maize equivalent yield (MEY) by 13% over CT and improved soil bulk density. Residue retention and NE+GS enhanced MEY by 2.4% and 5.5-11.3%, respectively. PRB improved net returns by similar to 27%, while NE+GS achieved the highest profitability and energy-use efficiency. Soil biological indicators were significantly higher under PRB, +R, and NE+GS. The soil quality index (SQI) improved by 6% under PRB and by 3.8-9.3% under NE+GS. Conclusions: Integrating PRB, residue retention, and precision nutrient management enhanced yield, profitability, energy-use efficiency and soil health in the M-W system. These CA-based combinations offered clear synergies with minimal trade-offs, contributing to both productivity and ecological sustainability. Implications: This study demonstrates that adopting CA-based practices can strengthen the resilience, resource-use efficiency, and long-term sustainability of M-W system under climate stress. The findings provide evidence-based guidance for scaling up CA-interventions across South Asia to achieve sustainable intensification in cereal-based systems.