The Sustainable Cocoa Production Program (SCPP) quantified carbon stocks from four pools: above-ground, below-ground biomass, litter and soil organic carbon in 30 farms of three cocoa shade management systems in West Sulawesi, Indonesia. Each shade management system was selected according to the number of shade tree species moving from the less to the more complex agroforestry system. The carbon footprint was estimated based on 51,620 farmers from the CocoaTrace farm management software, considering only the GHG emitted by the use of fertilizer.