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 on sites in two ecozones of SSA, the dry savanna (lna, Republic of Benin) and rainforest (Ilesha, Nigeria). Both sites were cultivated with two indigenous vegetable species: local amaranth (Amaranthus cruentus (AC)) and African eggplant (Solanum macrocarpon (SM)). The soils were treated with 5 t/ha poultry manure and urea fertilizer at the rates 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 AC 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 AC. Soils of the rainforest (RF) cultivated with AC 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 was 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 increasing the proportion of adsorbed P.