Cacao cultivation is rapidly increasing in Latin America under the influence of public policies and external markets. In Ecuador, the cultivated surface of high quality cacao trees has doubled in the last 50 years, creating great expectations in neighboring countries. Here, we investigated the social-ecological sustainability of cacao-based agroforestry systems in four rural Amazonian highlands communities in eastern Ecuador, close to the region where cacao was once domesticated. Kichwa-and Shuar-speaking groups were interviewed by adapting Ostrom's institutional diagnostic framework for social-ecological systems. Through a set of specifically created indicator variables, we identified key interactions and outcomes to understand the fragility and the sustainability of those communities. The studied communities were fairly young, with land rights secured less than 30 years ago in most cases. Per-family surfaces were very restricted (typically one hectare) and plots were divided between cash producing crops and their own home food. The small production per household goes through a precarious commercialization by both intermediaries and cooperatives, making the cacao bean production merely sufficient for pocket money. Ties with specialist producers in one community close to the capital has promoted the use of native cacao lines. Elsewhere, improved varieties of high productivity are planted along native trees being commercialized indistinctly. The continuity of these communities currently depend on a reorganization of their demography with parts of the population working elsewhere, as cacao bean production alone will continue to be insufficient, and will compete with their food self-sufficiency.