Continuous cultivation of rice–wheat cropping system in the Indo-Gangetic plains is under threat with decline in soil organic carbon (SOC), total factor productivity and overall sustainability. Pulses, an important component of crop diversification, are known to improve soil quality through their unique ability of biological N2 fixation, leaf litter fall and deep root system. Therefore, the effect of inclusion of pulses in the puddled rice system under organic and inorganic amendments on SOC pool and its management indices were evaluated in a long-term experiment after seven cropping cycles. The results indicated that inclusion of pulses in the rice-based system improved the SOC content, being greater in surface soil (0–20 cm) and declining with soil depth. Among the four carbon fractions determined, less labile carbon fraction (Cfrac3) was the dominant fraction in the puddled rice system, particularly under organic treatments, indicating that it is possible to maintain organic carbon for longer time in this system. The rice–wheat–mung bean system resulted in 6% increase in SOC and 85% increase in soil microbial biomass carbon as compared with the conventional rice–wheat system. Application of crop residues, farm yard manure (5 t ha−1) and biofertilisers had greater amount of carbon fractions and carbon management index (CMI) over control and the recommended inorganic (NPKSZnB) treatment in the soil surface, particularly in the system where pulses are included. Interestingly, in the puddled rice system, passive carbon pool is more in surface soil than deeper layers. The relative proportion of active carbon pool in surface layer (0–20 cm) to subsurface layer (20–40 cm) was highest in rice–wheat–rice–chickpea (1.14:1) followed by rice–wheat–mung bean (1.07:1) and lowest in the rice–wheat system (0.69:1). Replacing wheat with chickpea either completely or during alternate year in the conventional rice–wheat system also had positive impact on SOC restoration and CMI. Therefore, inclusion of pulses in the rice-based cropping system and organic nutrient management practices had significant impact on maintaining SOC in an Inceptisol of the Indo-Gangetic plains of India.