In the Amazon, the Yasuní Biosphere Reserve (YBR) is considered a natural and cultural diversity hotspot. It is populated by several indigenous groups, including the Kichwa, who are characterized by their traditional systems of production, which are a means of subsistence and socio-ecological integration. The objective of this research was to evaluate the sustainability of small farmers who use a traditional agroforestry system (chakra) within the buffer, transition, and core zones of the YBR. We conducted 133 interviews with Kichwa heads of households. The socio-demographic structure and distribution were identified, and the response-inducing sustainability evaluation (RISE) methodology was used to evaluate chakra sustainability according to social, economic, and ecological dimensions, expressed using 10 indicators from 50 parameters, valued from 0 (worst case) to 100 (best case). The results are expressed in a polygon, defined by the areas: (1) good performance, (2) medium performance, and (3) poor performance. We employed the multivariate classification hierarchical cluster technique and analysis of variance (ANOVA) to identify dissimilarities between groups of chakras and the existence of statistical differences, respectively. Among the studied indigenous Kichwas, a pyramidal structure progressive type was identified, which is characteristic of young populations and the nonexistence of significant differences between the RISE indicators and chakras. The lowest-scoring indicators using the RISE guidelines were: use of materials and environmental protection, animal production, economic viability and chakra administration. We provide suggestions for decision makers who support Kichwa populations in socio-productive management with sustainability goals. We to taking actions on the indicators identified with high priority to improve the sustainability in the chakras and sociodemographic dynamics.