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This article introduces a flexible, multi-scale framework for assessing sustainability in agroecological food systems that explicitly incorporates indicators of biopsychosocial well-being across the levels of individuals, communities and institutions, and economics and ecologies. We seek to operationalize the interactive relationship between biopsychosocial health and sustainability, and argue that well-being constitutes a critical service that underpins the resilience and long-term viability of food systems. Our proposed framework bridges psychological, social, and ecological sciences, leveraging participatory and transdisciplinary methodologies. It integrates two complementary sets of metrics: a primary series of validated and standardized tools designed to quantify the different levels (from individual to ecological) and a second, participatory, community-defined set of indicators we term “vital signs of place”. These context-sensitive indicators, developed through collaborative and participatory processes, seek to support epistemic justice by centering diverse ways of knowing and living. To ensure the framework remains actionable and avoids becoming a black box, we emphasize parsimony and practical feasibility in the selection of indicators. A deliberately limited and well-prioritized set of metrics enables meaningful implementation, supports stakeholder engagement, and facilitates interpretation across contexts. The resulting framework balances comparability across regions with adaptability to local priorities and is applicable at multiple scales—from watersheds to regional levels. Central to our approach is the conceptualization of well-being as the dynamic expression of self-directedness, cooperativeness, and self-transcendence both in individuals and communities, following C. Robert Cloninger's biopsychosocial model of personality. This view highlights well-being not merely as a state, but as a developmental process emerging from purposeful agency, social connectedness, and a sense of meaning beyond the self—across individuals, communities, and institutions. We emphasize as well the interactive role of socio-ecological organization in encouraging, or discouraging, these dimensions of well-being. The different standardized metrics and participatory indicators are looked at from this perspective. By focusing on the lived experiences and biopsychosocial health of rural communities, our approach aims to contribute to long-term sustainability efforts and addresses key challenges related to the Sustainable Developmental Goals. This framework offers tools and actionable guidance for researchers, policymakers, and practitioners seeking to center well-being in the transformation of the socio-ecological organization of food systems.