Soil is a large sink for carbon (C), with the potential to significantly reduce the net increase in atmospheric CO₂ concentration. However, we previously showed that subtropical tree plantations store less C into long-term soil pools than rainforest or pasture. To explore reasons for differences in C storage between different land-use systems, we examined the relationships between soil aggregation, iron and aluminium oxide and hydroxide content, and soil organic C (SOC) under exotic C₄ pasture (Pennisetum clandestinum), native hoop pine (Araucaria cunninghamii) plantations, and rainforest. We measured SOC concentrations of water-stable and fully dispersed aggregates to assess the location of soil C. Concentrations of dithionite- and oxalate-extractable iron and aluminium were also determined to assess their role in SOC sequestration. Soil under rainforest and pasture contained more C in intra-aggregate particulate organic matter (iPOM, >53 μm) than hoop pine plantations, indicating that in rainforest and pasture, greater stabilisation of SOC occurred via soil aggregation. SOC was not significantly correlated with dithionite- and oxalate-extractable Fe and Al in these systems, indicating that sorption sites of Fe and Al oxides and hydroxides were saturated. We concluded that soil C under rainforest and pasture is stabilised by incorporation within soil aggregates, which results in greater storage of C in soil under pasture than plantations following land-use change. The reduced storage of C as iPOM in plantation soil contributes to the negative soil C budget of plantations compared with rainforest and pasture, even 63 years after establishment. The results have relevance for CO₂ mitigation schemes based on tree plantations.