This study investigated the effects of different land-use systems (LUS) and soil management practices (SMP) on soil aggregate stability and the distribution of soil organic carbon (SOC) and nitrogen (N) among aggregate size fractions. The long-term effects of plantation crops (tea and bamboo), horticultural systems (mango and lemon) and conventional agricultural cropping systems (rice–rice, wheat–millets and okra–onion) were evaluated in northeastern India. Soil organic carbon and total nitrogen (TN) were quantified within different aggregate size fractions to assess the influence of LUS and SMP on carbon and nitrogen stabilization. The results showed that uncultivated land exhibited the lowest mean weight diameter (MWD) of aggregates (0.69 mm), while mango land-use recorded the highest value (0.96 mm). Surface soil under tea plantations exhibited the highest TN concentration (1.31 g kg-1), closely followed by mango plantations; both were significantly higher than the concentrations observed in agricultural systems. Across all LUS, macroaggregates were found to hold greater SOC than microaggregates. Notably, tea plantations had the highest SOC levels within microaggregates (13.2 g kg-1), followed by bamboo, highlighting their superior capacity for stabilizing organic carbon. The distribution of total nitrogen within macroaggregates mirrored the pattern observed for SOC. Elevated clay-associated SOC under tree-based systems (tea, mango and bamboo) suggests enhanced long-term carbon stabilization due to the longer residence time of clay-bound organic matter.