The build‐up of topsoil phosphorus (P) through excess fertilizer application can increase P losses in run‐off leading to negative impacts on aquatic ecosystems. To better understand the risk of P losses, the fractions of soil P in four aggregate size classes were quantified for two vegetable production sites (<10 and >25 yrs) and a conservation buffer site (8 yrs) in southwestern China. Sequential extraction methods of inorganic P (Pi) and organic P (Po) were carried out on samples from Nitisol and Gleysol soils from 0 to 5 cm and 5 to 10 cm depths. On average, soil Pi concentrations exceeded Po concentrations threefold, primarily in the bioavailable Pi fractions (labile Pi, loosely bound Pi and non‐occluded Pi). Soil Po fractions and bioavailable Pi fractions were significantly greater under the >25 yrs field than in the <10 yrs field. The conversion of fields under vegetable production to forested buffer substantially decreased the levels of the bioavailable Pi and labile Po in the Gleysol after 8 yrs. Soil macro‐aggregates (>0.25 mm) had greater concentrations of bioavailable Pi fractions and of labile and moderately labile Po than did micro‐aggregates and silt and clay size components. Although more P was stored in recalcitrant P forms, a larger percentage of all P fractions was found in macro‐aggregates in these soils. Small active P‐enriched aggregates potentially intensify export of P from the vegetable soils by run‐off, and therefore, management practices must be optimized to enhance agricultural P efficiencies.