Crop diversification and their impact on soil C pools and C indices in Eastern plateau region of India is yet to be clearly understood. To explore this, a nineteen years field experiment was carried out to identify suitable diversified cropping system of this region with assessing the SOC pool, C and humification indices. Selected cropping systems were, uncultivated grassland (D-0), rice-fallow (D-1), rice-fallow/rice-okra/rice-maize (D-2), rice-fallow/rice-capsicum/rice-mungbean (D-3) and rice-fallow/rice-capsicum/rice-babycorn/rice-groundnut systems (D-4). Total organic carbon (TOC), various fractions of reactive and recalcitrant C pools, humification indices, dehydrogenase activity and carbon management index (CMI) were determined for 0−15, 15−30 and 30−45 cm soil layers. After 19 years of cultivation, SOC content (g kg−1) of the soil was improved by 22.9 % in D-1 system in 0−15 cm soil depth. Depth dynamics revealed decrement of SOC fractions and stocks with increasing soil depth, although minimum decrement has noticed in D-3 and D-4 systems. D-1 system had the highest very labile C (VLC), labile C (LC) stock, whileless labile C (LLC) and humus C (Hum-C) was found to be highest in D-0. In deeper soil layers (30−45 cm), D-4 system had the highest reactive C pool (RP) stock. Percent deviation of RP-C stock under D-4 system had also the lowest across the 45 cm soil profile. D-2, D-3 and D-4 systems had ∼34, 52 and 40 % higher C lability index (CLI) than D-0 in 0−15, 15−30 and 30−45 cm soil depths, respectively. Besides, D-1 system had similar and ∼ 63 % higher CMI value at 0−15 and 15−30 cm, while, ∼76 % higher CMI value was observed in D-4 system at 30−45 cm in respect to the reference. At lower depth, rate of humification and dehydrogenase activity were enriched in D-4 system. Thus D-4 can be considered as efficient agro-ecosystem to maintain temporal soil fertility and soil health. At regional scale, more diversified rice-based cropping system with legumesappears to be more promising cropping practice that sustains SOC with higher rate of humification and microbial activity.