Due to complex interactions, changes in any one area of food systems are likely to impact—and possibly depend on—changes in other areas. Here we present the first annual monitoring update of the indicator framework proposed by the Food Systems Countdown Initiative, with new qualitative analysis elucidating interactions across indicators. Since 2000, we find that 20 of 42 indicators with time series have been trending in a desirable direction, indicating modest positive change. Qualitative expert elicitation assessed governance and resilience indicators to be most connected to other indicators across themes, highlighting entry points for action— particularly governance action. Literature review and country case studies add context to the assessed interactions across diets, environment, livelihoods, governance and resilience indicators, helping different actors understand and navigate food systems towards desirable change.