This study combines two methodologies—key indicators from the Sustainable Livelihoods Framework (SLF) and the Sustainability Assessment of Food and Agriculture Systems (SAFA) approach—to evaluate sustainability among 330 producers from three associations working within the recently recognized Amazonian Chakra system, designated as a Globally Important Agricultural Heritage System (GIAHS). The SAFA framework's four dimensions—Good Governance, Environmental Integrity, Economic Resilience, and Social Well-being—were used to assess sustainability, while the SLF considered key capitals such as financial, natural, and human capitals as critical for understanding livelihood outcomes. The discriminant analysis revealed significant differences across the associations, with Kallari and Wiñak performing better in financial management, environmental practices, and governance compared to Tsatsayaku, which exhibited weaker outcomes in these domains. Key indicators such as chakra income, price determination, and civic responsibility were the most effective in distinguishing the groups. The income analysis further highlights that Tsatsayaku reported the highest total income but relies heavily on non-Chakra sources, while Kallari and Wiñak showed stronger reliance on Chakra income, which aligns with their more sustainable agricultural practices. Per-capita income was higher for Tsatsayaku, but extreme poverty levels remained similar across all associations, underscoring the need for targeted financial interventions. Policy recommendations include promoting access to financial resources and strengthening participatory governance models to enhance sustainability outcomes across associations. For future research, combining the SAFA and SLF provides a comprehensive and robust methodology for assessing sustainability in agricultural systems, enabling a deeper understanding of the interactions between social, economic, and environmental factors in diverse contexts.