Ecuador is the third largest cacao exporter in the world. Up to 10 % of Ecuador's cacao production is grown in the Amazon region, mostly under conventional (CA) and organic (OA) agroforestry systems. Despite the importance of cacao in this area, no previous studies on its environmental impact and economic viability have yet been carried out. The main objective of this research is to fill this gap and, more specifically, perform a comparative analysis between CA and OA systems. For this purpose, primary information was gathered from 90 farms (44 conventional and 46 organic ones) that implement land management practices. The environmental performance of cacao production was assessed using a life cycle analysis methodology, with a cradle-to-farm gate approach. Up to twelve impact categories and five environmental and monetary efficiency indicators were estimated based on three functional units (1 kg of cacao, 1 kg of output sold, and 1 ha). Additionally, an economic viability analysis was performed, focused on profitability. The results show that organic management allows to reduce the environmental impact in all the analyzed categories, except for the land footprint, and improved the environmental and economic efficiency of agroforestry systems. The economic analysis shows no statistically significant differences between CA and OA profitability (net margin), which can be improved by selling co-products. Despite the low environmental impact of both types of system, economic profitability is certainly one of the weaknesses of cacao production in the Ecuadorian Amazon region. This study contributes to develop technical, production-related and political actions that could improve the economic cacao production situation without jeopardizing the environmental benefit obtained by these systems.