This paper presents a new methodological approach to assess food systems which takes stock of strengths and limitations and tries to fill some of the gaps identified by recent publications. Its specificity is twofold: (i) to consider both national scale (where key policy decisions are made) and subnational scale (which provides a more comprehensive understanding of food systems), (ii) to articulate international quantitative indicators (providing comparativeness and long-term perspective), literature review and local stakeholders consultations to frame the sustainability issues and unravel the causal mechanisms within the system. After presenting the method, the paper draws lessons from its implementation in eight countries in Africa, Asia and Latino America. It proved to renew the existing methodologies regarding the consideration of subnational specificities and articulation of scales, highlighting the interactions between the different components of the system, and in terms of identifying main long-term trends. Yet, certain methodological challenges are remaining and deserve even greater attention in the future, notably regarding data availability, the differentiation of types of actors and their practices, and the involvement of the diversity stakeholders, including the less voiced one, in the analytical process.