This study investigated the speciation, transformation and availability of P during indigenous vegetable production by employing a combination of chemical and spectroscopic techniques. The study focused upon sites in two ecozones of SSA, the Dry Savanna (lna, Benin Republic) and Rainforest (Ilesha, Nigeria). Both sites were cultivated with two indigenous vegetable species; local amaranth (Amaranthus cruentus (AV)) and African eggplant (Solanum macrocarpon (SM)). The soils were treated with 5 t/ha poultry manure and urea fertilizer at the rate of 0, 20, 40, 60 and 80 kg N/ha. Soil samples were collected before planting and after harvest. Phosphorus K-edge X-ray absorption near-edge structure (XANES) spectroscopy was used to determine P speciation in these soils. Quantitative analysis showed that adsorbed and organic P were the two dominant P species in the manure amended Dry Savanna (DS) soils before planting and after harvest in soils cultivated with both AV and SM, with the addition of urea (40 kg N/ha) causing an increase in the organic P form in Dry Savanna soils cultivated with AV. Soils of the Rainforest (RF) cultivated with AV initially had large amounts of apatite P in the manure amended soils prior to planting which was transformed to adsorbed and organic P after harvest. Urea addition to the Rainforest soils shifted the dominant P species from organic P to adsorbed and apatite P, which is likely to limit P availability. Soils cultivated with SM had similar proportions of both organic and adsorbed P forms, with 40 kg N/ha addition slightly increased the proportion of adsorbed P.