Agroforestry systems (AFS) are economically viable and provide diverse ecosystem services. We studied the long-term effects of tree-based AFS on carbon and nitrogen pools in Punjab, India. The selected systems were poplar with fodder-wheat rotation (T1), eucalyptus with fodder-wheat rotation (T2), sole fodder-wheat rotation (T3), poplar with citrus (kinnow) (T4), eucalyptus with citrus (T5), sole citrus (T6) and fallow land (T7). At the 0-15 cm soil depth, T1 and T2 had 87.9 and 70.6% higher soil organic carbon (SOC), respectively, than T3, while T4 and T5 had 37.4 and 30.2% higher SOC, respectively, than T6. At all soil depths, SOC was lowest under fallow land and decreased with depth. The soil carbon pools (very labile, labile, less labile and recalcitrant carbon) were highly positively correlated with SOC and were higher in T1 and T2 than in other land-use systems. Water-soluble carbon, microbial biomass carbon, total N, ammonium N and nitrate N were highest in T1 and decreased with depth. Carbon management index was significantly higher in T1 and T2 than other systems. Therefore, poplar- and eucalyptus-based AFS with fodder-wheat rotation were more efficient in improving soil carbon and nitrogen status along with sustainability of the systems.