Conservation agriculture-based sustainable intensification (CASI) technologies comprising zero-tillage with crop residue retention (>30%) on the soil surface, diversified cropping systems, and balanced nutrient management are recognized as operative and efficacious strategies to ensure food security in the parts of South Asia. The present investigation was a component of CASI technologies undertaken in the farmers’ field of Malda (old alluvial Inceptisol) Coochbehar (recent alluvial Entisol) district, West Bengal (subtropical eastern India). This study was conducted to evaluate the short-term impact of contrasting tillage (zero and conventional) and cropping systems (rice-wheat and rice-maize) on total organic carbon (TOC) and its fractions, viz., labile pool-1 (LP1), labile pool-2 (LP2) and recalcitrant carbon (RC) fractions after 4-year trial of conservation agriculture (CA) in the old and recent alluvial soils. Soil samples were collected from three depths (0-5, 5-10, and 10-20 cm), and thus, our study was focused on two factors, viz., cropping system and tillage. Results pointed that TOC along with LP1, LP2, and RC fractions under rice-maize (RM) cropping system were significantly (p<0.05) greater (15-35%) over rice-wheat (RW) system as a result of higher residue biomass addition. Zero-tillage (ZT) improved the C fractions by 10-20% over conventional tillage (CT) in all aspects. TOC and its fractions were observed to be greater under the ZT system in the topmost soil depths (0-5 and 5-10 cm), but the same system failed to improve these at 10-20 cm. Interestingly, the CT increased all the fractions at 10-20 cm depth due to the incorporation of crop residues. The concentration of TOC along with its fractions decreased with increasing soil depth was evident. Comparatively, all the C fractions, including TOC were maximum in soils from Malda sites as compared to Coochbehar sites because of a higher amount of residue biomass application, higher clay content, and greater background content of C in these soils. All the studied C fractions showed a significant correlation (r = >0.635; p<0.01) with TOC among all the soil depths in both the districts but the relationship with soil texture showed some interesting results. TOC fractions were significantly correlated (p<0.01) with clay particles indicating that its higher stabilization with clay in old alluvial Inceptisol (Malda); while in recent alluvial Entisol (Coochbehar), sand particle showed its strong relation with TOC fractions. Higher stratification ratio (SR) in the ZT system suggested that the concentration of TOC and its fractions are confined to the upper soil layers whereas in the case of CT, by and large, the distribution of these was comparatively high in subsequent soil depths due to residue incorporation effect. The concentration of C fractions in soils followed the order: TOC > RC > LP2 > LP1. The present investigation concluded that ZT under the RM system increases the turnover rates of C in both soil types but the amount of clay influences the stabilization/storage of C.