Urbanization in the Global South presents challenges in developing effective strategies for addressing food security and waste management within agri-food-waste systems. This research proposes a strategic, multidimensional diagnosis of nutrient-flow management to support urban planning processes in metropolitan areas, integrating tools and principles from urban metabolism and urban planning. The framework was applied to the Metropolitan Region of Santiago, a regional forerunner in nutrient circularity capacity. Extensive data collection, including over 30 stakeholder interviews, revealed spatial, material, and social factors influencing nutrient flows across the regional agri-food-waste system. Outputs included systemic diagrams, Sankey diagrams, regional recovery and reuse indicators, stakeholder characterizations, and social network diagrams. The flow analysis revealed that wastewater treatment is the main source of nutrient loss, while imported animal feed dominated nutrient inputs. Reuse remains limited in high-demand areas like fruit production and pig feed, linked to regulatory, technological, and logistical barriers. Subsystem activities follow clear urban–rural patterns, which align with spatial nutrient imbalances. The social analysis identified over 45 key stakeholders, distinguishing actors central to improving recovery (e.g., municipalities, WWTPs) versus reuse (e.g. rendering industries). It also highlighted weakly connected institutions (e.g. Ministry of Housing and Urbanism), suggesting coordination gaps. Regional indicators reveal that while urban nutrient recovery is relatively high (72 %), agricultural reuse remains low (12 %), underscoring inefficiencies in reintegrating secondary nutrients into food systems. Bridging actors and policies across rural and urban domains will be essential for improving coordination and addressing territorial nutrient imbalances. This diagnostic supports context-specific planning strategies for advancing nutrient circ