Phosphorus (P) is a limiting element in highly-weathered subtropical/tropical soils. Depending on lithology, tropical soils differ strongly in soil chemistry and aggregate structure but little is known about how this controls P speciation and distribution and hence P supply for the forests. We compared the distribution of organic and inorganic P fractions as well as microbial biomass P (MBP) and enzymatic activities in bulk soils and soil aggregates of two adjacent subtropical forests, one on an acidic red soil and one on a limestone soil. The red soil was poor in total P (TP) and exchangeable P (Ex-P) but rich in iron-bound (Fe-P) and MBP, phosphorus in the limestone soil was more evenly distributed among different P fractions conveying an overall larger P availability. We found major differences in P abundance and distribution in macro- and micro- aggregates between the soils: 1) red soil was dominated by stable organic P which was slightly enriched in macro-aggregates, while limestone soil held higher proportion of labile organic P with organic P fractions being more equally distributed across aggregate sizes. 2) MBP was more abundant in red soil and, like organic P, concentrated in macro-aggregates, while MBP in limestone soil was concentrated in micro-aggregates. MBP correlated positively with other P forms in the macro-aggregates of the red soil, whereas it correlated negatively in the macro-aggregates of the limestone soil. 3) Phosphatase and phytase activities correlated positively with organic P forms in both macro- and micro-aggregates of the red soil but not in the limestone soil. Together, these findings indicate that microorganisms mediate a tighter P cycle in the P-poor red soil. In the P-rich limestone soil, macro-aggregates appear to protect P from microbial uptake by calcium adsorption and occlusion, hence contribute to P sequestration. Our study highlights the key role of lithology for controlling P storage and supply in subtropical forest soils, which is relevant for forest conservation and restoration.