Stabilisation and protection of soil organic carbon (SOC) in macroaggregates and microaggregates represents an important mechanism for the sequestration of SOC. Legume-based grass pastures have the potential to contribute to aggregate formation and stabilisation, thereby leading to SOC sequestration. However, there is limited research on the C and N dynamics of soil organic matter (SOM) fractions in deep-rooted legume leucaena (Leucaena leucocephala)–grass pastures. We assessed the potential of leucaena to sequester carbon (C) and nitrogen (N) in soil aggregates by estimating the origin, quantity and distribution in the soil profile. We utilised a chronosequence (0–40 years) of seasonally grazed leucaena stands (3–6 m rows), which were sampled to a depth of 0.3 m at 0.1-m intervals. The soil was wet-sieved for different aggregate sizes (large macroaggregates, >2000 µm; small macroaggregates, 250–2000 µm; microaggregates, 53–250 µm; and <53 µm), including occluded particulate organic matter (oPOM) within macroaggregates (>250 µm), and then analysed for organic C, N and δ13C and δ15N. Leucaena promoted aggregation, which increased with the age of the leucaena stands, and in particular the formation of large macroaggregates compared with grass in the upper 0.2 m. Macroaggregates contained a greater SOC stock than microaggregates, principally as a function of the soil mass distribution. The oPOM-C and -N concentrations were highest in macroaggregates at all depths. The acid nonhydrolysable C and N distribution (recalcitrant SOM) provided no clear distinction in stabilisation of SOM between pastures. Leucaena- and possibly other legume-based grass pastures have potential to sequester SOC through stabilisation and protection of oPOM within macroaggregates in soil.