To increase the limited knowledge about phosphorus (P) species in strongly weathered soils of agroforests in tropical regions, the soil organic P was determined in different cacao (Theobroma cacao L.) agroforestry systems from the Atlantic forest region of Brazil, varying in age and phosphate fertilizer application. For this purpose NaOH-EDTA extraction and solution 31P nuclear magnetic resonance spectroscopy (31P NMR) were used. The studied areas were agroforests with different management systems: cacao-cabruca, cacao + erythrina, and cacao + rubber tree, which were compared with unfertilized pasture and natural forest. The results show that the distribution of P species in soil varied according to the different management practices (P fertilization, tree species and tree density) and stability time (different ages) of the cacao agroforests with low input of phosphate fertilizer. In cacao agroforests, natural forest and pasture a large portion of soil organic P (Po) consisted of P-monoester with lower concentrations of DNA. This Po species was correlated positively with clay and soil organic carbon. However, the recent conversion of natural forest and pasture to cacao agroforests led to a decrease in DNA concentration. High concentrations of pyrophosphate found in all cacao agroforests could be an evidence of a high soil fungal activity in cycling and accumulation of this P species. Moreover, the high concentrations and relative proportions of Po and pyrophosphate species revealed a high potential of P supply to trees in case of suppression of the phosphate fertilization in these agroforestry systems.