There is increasing demand for agricultural commodities that are produced in a climate-friendly manner. At the same time, in many or most tropical countries there is need for intensification of agricultural production to increase yields and incomes, and this usually requires higher external inputs that may cause additional greenhouse gas emissions. Here we investigate if production methods that have a beneficial effect on the climate (are climate-friendly) are compatible with increased inputs and yields for traditional, shaded cocoa (Theobroma cacao) production systems (locally known as cabrucas) in southern Bahia, Brazil. We use two easily measurable and manageable dimensions of climate friendliness, namely the carbon (C) stocks in the large trees and the C footprint as related to on-farm agrochemical and fuel use. Through interviews and field inventories in 26 cabruca farms representing a range of production practices and intensities, we identify the combinations of management practices, yields, C stocks and C footprints typically found in the region. We find that yield levels up to the highest encountered yield of 585 kg ha−1, or twice the current regional average of 285 kg ha−1, are compatible with an aboveground C stock in the large shade trees (>30 cm diameter at breast height) of up to 65 Mg ha−1 and up to 55 % shade. Higher C stocks and shade levels are generally associated with yields below the regional average. Input-related C emissions increased non-linearly with increasing yield, but even the highest encountered yields were compatible with low (<0.25 kg CO2e kg−1 of cocoa) to medium (<0.5 kg CO2e kg−1 of cocoa) input-related emission levels. Cocoa yields responded positively to increased fertilizer applications, provided that other factors, including shade levels, were not limiting. Consequently, the highest input-related emissions (>1 kg CO2e kg−1 of cocoa) were related to large fertilizer applications that did not proportionately increase yields. We conclude that doubling the cocoa output from southern Bahia, where cabrucas are the predominant form of growing cocoa, is compatible with climate-friendly production practices, measured by local standards. We suggest that the presented methodology can be used to identify opportunities for climate-friendly intensification of tree crops more generally, thereby increasing the contribution of commodity production to global climate change mitigation.