The expansion of conventional agricultural models in the Colombian Amazon has caused deforestation, biodiversity loss, and socio-environmental degradation. In response, agroecology and bioeconomy are emerging as key strategies to regenerate landscapes and foster sustainable production systems. We evaluated the agroecological performance of 25 farms in the Andean–Amazon transition zone of Colombia using FAO's Tool for Agroecology Performance Evaluation (TAPE). The analysis included land cover dynamics (2002–2024), characterization of the agroecological transition based on the 10 Elements of Agroecology, and 23 economic, environmental, and social indicators. Four farm typologies were identified; among them, Mixed Family Farms (MFF) achieved the highest transition score (CAET = 60.5%) and excelled in crop diversity (64%), soil health (SHI = 4.24), productive autonomy (VA/GVP = 0.69), and household empowerment (FMEF= 85%). Correlation analyses showed strong links between agroecological practices, economic efficiency, and social cohesion. Land cover dynamics revealed a continuous decline in forest cover (12.9% in 2002 to 7.1% in 2024) and an increase in secondary vegetation, underscoring the urgent need for restorative approaches. Overall, farms further along the agroecological transition were more productive, autonomous, and socially cohesive, strengthening territorial resilience. The application of TAPE proved robust multidimensional evidence to support agroecological monitoring and decision-making, with direct implications for land use planning, rural development strategies, and sustainability policies in the Amazon. At the same time, its sensitivity to high baseline biodiversity and to the complex socio-ecological dynamics of the Colombian Amazon underscores the need to refine the methodology in future applications. By addressing these challenges, the study contributes to the broader international debate on agroecological transitions, offering insights relevant for o