While there is a consensus on the need to transition towards more sustainable food systems, moving from a conceptual approach to a more operational understanding of food systems remains a research front. The objective of this paper is to take stock of existing methods to assess the sustainability or resilience of food systems. To grasp the diversity of the methods, we built a typology based on 33 documents identified through a scoping review. The critical analysis of our typology reveals several blind spots and the need for more systemic, consultative and multiscale methodologies, which consider the diversity of knowledge to disentangle the interdependencies between different components of the systems, in order to effectively support policy dialogue and decision making.