Information concerning the classification of soils and their properties under cacao agroforestry systems of the Atlantic rain forest biome region in the Southeast of Bahia, Brazil is largely unknown. Soil and climatic conditions in this region are favorable for high soil carbon storage. This study is aimed to classify soils under cacao agroforestry and further, to quantify carbon stocks in these soil profiles. Soil classification was performed, and the amount of C stored was estimated, based on the thickness of the soil horizons, their bulk density, and total organic carbon stored. In the sites studied under cacao, four general classes of soils were identified: Ultisols, Oxisols, Alfisols, and Inceptisols. Carbon stocks in these soil profiles showed wide variation, ranging from 719.24 to 2089.93 Mg ha−1. Carbon stocks in soil surface and subsurface layers in different agroforestry systems with cacao (cacao cabruca, cacao × rubber tree, and cacao × erythrina) were comparable; however, total storage of organic C in these soils was higher than expected, compared to values reported for the International Soil Reference and Information Center (ISRIC), based on the FAO-UNESCO database, and were also higher than estimated regional soil data.