Tropical forests store a large part of the terrestrial carbon and play a key role in the global carbon (C) cycle. In parts of Southeast Asia, conversion of natural forest to cacao agroforestry systems is an important driver of deforestation, resulting in C losses from biomass and soil to the atmosphere. This case study from Sulawesi, Indonesia, compares natural forest with nearby shaded cacao agroforests for all major above and belowground biomass C pools (n = 6 plots) and net primary production (n = 3 plots). Total biomass (above- and belowground to 250 cm soil depth) in the forest (approx. 150 Mg C ha^-1) was more than eight times higher than in the agroforest (19 Mg C ha^-1). Total net primary production (NPP, above- and belowground) was larger in the forest than in the agroforest (approx. 29 vs. 20 Mg dry matter (DM) ha^-1 year^-1), while wood increment was twice as high in the forest (approx. 6 vs. 3 Mg DM ha^-1 year^-1). The SOC pools to 250 cm depth amounted to 134 and 78 Mg C ha^-1 in the forest and agroforest stands, respectively. Replacement of tropical moist forest by cacao agroforest reduces the biomass C pool by approximately 130 Mg C ha^-1; another 50 Mg C ha^-1 may be released from the soil. Further, the replacement of forest by cacao agroforest also results in a 70-80 % decrease of the annual C sequestration potential due to a significantly smaller stem increment.