In lowland rice agroecosystems, inefficient resource utilization has led to reduced agricultural productivity and increased greenhouse gas emissions, particularly methane from flooded paddy fields. Alternative systems, such as rice-green gram under resource conservation practices, are underexplored in eastern India, where energy-intensive, high-emission, low-productivity rice-rice and rice monocropping systems prevail. This study is the first to demonstrate that a rice-green gram system with resource conservation technologies can improve soil health, reduce emissions, and increase productivity. A field study conducted during the 2014–2015 and 2015–2016 cropping seasons, part of a long-term experiment beginning in 2011-2012, compared six resource conservation technologies, including brown manure, green manure, wet drum seeding, zero tillage, green manure with real-time nitrogen, and biochar, to conventional practices. Key metrics assessed included system yield, greenhouse gas emissions, soil organic carbon stocks, and energy savings across different seasons. Zero tillage showed the highest carbon sequestration rate (0.97 Mg ha−1 yr−1), significantly increased soil organic carbon levels, and provided substantial energy savings (52.0 to 67.8%) while exhibiting the lowest global warming potential. Green manure also increased soil organic carbon and crop yields but was associated with higher greenhouse gas emissions compared to other practices. Overall, all resource conservation technologies improved system productivity and soil organic carbon stocks compared to conventional practices. The findings suggest that zero tillage and green manure are particularly effective in enhancing soil organic carbon levels and reducing greenhouse gas emissions in lowland rice-based cropping systems. Zero tillage, especially, stands out as a sustainable agricultural practice, offering a promising approach to mitigating methane emissions and achieving long-term soil carbon storage. The adoption of these practices can therefore contribute significantly to the sustainability and resilience of agricultural systems, paving the way for climate-smart agriculture that balances productivity with environmental sustainability.