The current expansion of cacao cultivation in the Republic of Côte d’Ivoire is associated with deforestation, forest degradation, biodiversity loss and high greenhouse gas (GHG) emissions. Global concerns about emissions that are associated with tropical commodity production are increasing. Consequently, there is a need to change the present cacao-growing practice into a more climate-friendly cultivation system. A more climate-friendly system causes lower GHG emissions, stores a high amount of carbon in its standing biomass and produces high cacao yields. GHG emissions and carbon stocks associated with the present cacao production, as assessed in 509 farmers’ fields, were estimated by using the Perennial GHG model and the Cool Farm Tool. On average, the production of 1 kg cacao beans is associated with an emission of 1.47 kg CO2e. Deforestation contributed largely to GHG emissions, while tree biomass and residue management contributed mainly to carbon storage. The collected data combined with the model simulations revealed that it is feasible to produce relatively high yields while at the same time storing a high amount of carbon in the standing biomass and causing low GHG emissions. The climate-friendliness of cacao production is strongly related to farm management, especially the number of shade trees and management of residues. Calculated emissions related to good agricultural practices were 2.29 kg CO2e per kg cacao beans. The higher emissions due to the use of more agro-inputs and other residue management practices such as recommended burning of residues for sanitary reasons were not compensated for by higher yields. This indicates a need to revisit recommended practices with respect to climate change mitigation objectives.