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Soil health is central to agroecological transitions, yet guidance for integrating it into agri-food system design and monitoring remains fragmented. Institutions increasingly use frameworks to define indicators, guide interventions, and report progress against climate, biodiversity, and food-security agendas. However, to our knowledge, there is no integrative soil health framework which coherently links biophysical diagnostics, socio-institutional enablers, and multiscale accountability. This leaves critical gaps in design, sequencing, and measurement of agroecological transitions. Here we review how soil health is operationalized within agroecology and agri-food systems and translate these patterns into an actionable programming guide. We reviewed 64 frameworks and extracted 652 indicators across 12 agroecological principles to build a framework-by-principle evidence matrix. Frameworks were classified by use-orientation (theory, practice, analysis), and indicator thematic profiles were analyzed using hierarchical clustering with adaptive branch detection. The major findings are as follows: (1) framework evolution exhibits four chronological waves with shifts from conceptual foundations to operational measurement and outcome reporting, alongside changes in global and regional agenda setting and a rising demand for comparable indicators; (2) clustering identified five soil health design domains separating biophysical and socio-economic principles and revealing stable micro-constellations beyond earlier pathway framing. These include soil management and input stewardship, soil-health assessment, agroecological and ecosystem-based, integrated landscape and livelihood, and policy- and outcome-based. These findings were translated into a sequenced, multi-domain programming architecture that operationalizes complementarity across diagnostics, stewardship implementation, ecosystem safeguards, landscape–livelihood embedding, and iterative learning, thereby closing the gaps between farm practices, governance mechanisms, and outcome monitoring for soil health.