Agrifood systems are called upon to undergo profound transformation. The development of “flow approaches” (including lifecycle assessment, carbon footprint, ecological footprint, and metabolism methodologies) has been crucial to point to the material side of human activities. More specifically, these approaches highlight the material and energetic costs of long agrifood value-chains, intensive farming practices, high levels of geographic specialization, as well as the production of non-food commodities. In the logical progression from diagnosis to action, flow approaches are currently being used as decision-support tools. But what are the biases induced by flow approaches when it comes to supporting real-world transformations? Based on our experience and interdisciplinary background, we argue that flow approaches provide a decontextualized and narrow framing of issues related to agrifood systems, such as accumulations and transfers across space and time, inequalities and asymmetries along the chain of activities, or long-lasting environmental impacts. Some aspects are measured and emphasized, while others are difficult to observe or neglected. Flow approaches, alone, are not well suited to inform issues of environmental justice, radical transformation, and local governance. As in most cases methodological advances will not suffice to overcome the biases induced; we call for hybridizing methods and for broadening analytical perspectives.