Deterioration of soil physical quality and depletion of soil organic carbon (SOC) are widespread challenges in tropical rice–wheat growing regions. Consequently, soil productive capacity, production sustainability, and resource use efficiency have declined in this agro-ecosystem. Ecological engineering approach such as legume inclusion in cropping system offers several ecosystem services, and thus, may serve an important role in the restoration of soil health. Given that, a long-term (2003–2015) field experiment was conducted to assess the impact of four rice-based crop rotation treatments [rice–wheat, rice–chickpea, rice–wheat–mungbean, rice–wheat–rice–chickpea] each with three levels of nutrient management treatments [control, integrated nutrient management, chemical fertilizers] on soil aggregation, soil carbon pools, and carbon stabilization. Legume inclusive rotations increased water stable macro-aggregates (WSMA) over rice–wheat rotation in both surface (0–0.2 m) and subsurface (0.2–0.4 m) soil depths. In surface soil, WSMA was the highest in rice–wheat–mungbean rotation (65%) followed by rice–chickpea rotation (57%) and was the least in rice–wheat rotation (50%). Subsequently, grain legume inclusive rotations had the higher aggregate ratio and mean weight diameter over rice–wheat rotation, being the highest in rice–wheat–mungbean rotation. Rice–wheat–mungbean and rice–chickpea rotations had higher carbon concentration in coarse macro-aggregates, meso-aggregates, and coarse micro-aggregates as compared with rice–wheat rotation. Grain legume inclusive rotations increased active carbon pool (9–18%), SOC (6–17%), and carbon management index (5–7%) over rice–wheat rotation, and the order was rice–wheat–mungbean > rice–chickpea ≥ rice–wheat–rice–chickpea > rice–wheat. Integrated nutrient management treatment resulted in higher macro-aggregate (7%), mean weight diameter (6%), active carbon pool (22%), passive carbon pool (16%), SOC (20%), and carbon management index (22%) over the chemical fertilizer treatment. Thus, it is concluded that inclusion of grain legume in lowland rice-based rotation and integrated nutrient management could improve soil aggregation, carbon concentration in aggregates, and soil carbon pools in the tropical soils. The study highlights the prospects of strategic designing of legume inclusive rotation/s for rice agro-ecosystem health and its sustainability.