To reorient food systems to ensure they deliver healthy diets that protect against multiple forms of malnutrition and diet-related disease and safeguard the environment, ecosystems, and natural resources, there is a need for better governance and accountability. However, decision-makers are often in the dark on how to navigate their food systems to achieve these multiple outcomes. Even where there is sufficient data to describe various elements, drivers, and outcomes of food systems, there is a lack of tools to assess how food systems are performing. This paper presents a diagnostic methodology for 39 indicators representing food supply, food environments, nutrition outcomes, and environmental outcomes that offer cutoffs to assess performance of national food systems. For each indicator, thresholds are presented for unlikely, potential, or likely challenge areas. This information can be used to generate actions and decisions on where and how to intervene in food systems to improve human and planetary health. A global assessment and two country case studies-Greece and Tanzania-illustrate how the diagnostics could spur decision options available to countries.