Sustainable food security represents a significant challenge in advancing the global agenda expressed in the Sustainable Development Goals, including feeding the growing world population while transitioning toward a circular economy. A growing body of literature is focused on developing concepts and documenting circular economic opportunities in agricultural food systems. However, the methodologies for implementing circular economy models at the farm level remain mostly theoretical. This study proposes a transdisciplinary based approach for evaluating circular economy alternatives in agri-food systems while enhancing farmers’ decision-making skills. The transdisciplinary based research methodology combines methods for simulating critical resource and production flows with multi-criteria decision-making, including training and obtaining feedback from farmers. We test the methodology on a cacao agri-food system in Meta (Colombia). Biomass waste and cost-benefit data allow evaluation for decision-making of four circular economy scenarios: composting, vermicomposting, drip irrigation, and valorization of cacao husks. Research outcomes recommend vermicomposting as a viable circular economy innovation for cacao farms to reduce biomass waste and improve economic income at farm level. Other outcomes include capacity building of farmers on circular economy –including resource flow analysis and cost-benefit calculation. Effective decision-making on circular economy adoption at farm level is evidenced by vermicomposting technology implementation. Policy recommendations call for transdisciplinary based approaches for promoting and scaling the transition towards a circular economy in agri-food systems at a farm scale involving farmers participation in operations research (analytics) modelling and interpretation. In addition, policy advise for circular economy technical assistance and finance, includes vermicomposting as a technology for scaling transition of agri-food systems such as cacao and comparable long-term crops.