In southern Bahia, Brazil’s traditional cacao region, cacao is mostly grown under the shade of thinned Atlantic Forest (known as cabruca). These agroforestry systems are gradually being replaced by unshaded cacao monocultures that might be more vulnerable to changes in climate; however, the impacts of climate change have not been evaluated yet. We assessed the impact of climate change on the climatic suitability of cacao plantations in southern Bahia and evaluated to what extent the cabrucas reduce the vulnerability of cacao as compared to unshaded plantations. We measured the maximum temperature in a gradient of canopy cover during the warmest month of the year and projected ecological niche models (MaxEnt) on climate projections for 2050 simulating the microclimate of three production systems: cabrucas, intermediate shading, and unshaded plantations. We found that canopy cover drastically reduces daily maximum temperature, so that understory temperature in cabrucas can be up to 6.0 °C lower than in unshaded plantations. We show for the first time that all projected environmental changes negatively affect cacao in southern Bahia, diminishing its climatic suitability and reducing overall suitable areas across the region. More importantly, this study is the first one to show that cabrucas can reduce the negative impacts of climate change for cacao, especially where temperature extremes approach or exceed crop tolerance limits. We conclude that maximizing short-term profits by implementing unshaded monocultures will likely lead to production losses in the long term. Cabrucas have a central role in reducing the vulnerability of cacao to climate change and since these traditional agroforestry systems cannot be quickly restored, their conservation should be an important goal of agricultural policies in the region.