Amazonian Dark Earths (ADE), in general, have been enriched in their soil fertility with long-term deposition of a mixture of natural sediment and debris from human occupation. In particular, high total calcium (Ca) and phosphorus (P) contents and availability have been observed in most ADE soils. Phosphorus forms and transformation process in soil are critical in determining long-term soil fertility in such ADE soils, that otherwise are highly weathered and infertile. This study investigated soil P fractions present in ADE soils at different chronological ages (up to 6700 years BP) compared to adjacent non-ADE soils (Oxisols), and inferred transformation distribution of the biogenic calcium-phosphate (Ca-P) species and other P species in soil over time. Phosphorus sequential fractionation results showed higher proportions of Ca-bound inorganic P species than other fractions in younger ADE soils (<1100-2800 years BP). Phosphorus K-edge X-ray absorption near-edge structure (K-XANES) spectra coincided the fractionation results and indicated that Ca-P species present in younger ADE soils were indeed in more crystalline forms than those species in older soils (>2800 years BP). The results from both techniques verified that P species had been transformed from insoluble Ca-bound P species to soluble Ca-P species and to those adsorbed on iron- and aluminum-oxides both in inorganic and organic forms after considerable amount of time progressed. This study helps understand more about ADE soils, especially the dynamics of different P species in soil, thus one must be careful in management of such soils, otherwise causing destruction of ecological importance of ADE soils.