This article proposes a characterization of the European regulatory process for health claims, as well as an analysis of the controversy surrounding the methodological and evidentiary requirements for scientific substantiation. The study of regulations and relevant scientific papers looks at three issues: the epistemic policies adopted by the European Food Safety Authority, their possible implications for different areas, and proposals for alternative strategies presented by critics’ approaches. The hierarchy of evidence and methodologies defined by the regulation establishes that proving causality on the basis of randomized controlled trials is crucial for the authorisation of a claim. However, this standard of proof might be not suitable for investigating the effects of ingredients in nutrition science, promoting research, development and innovation in the functional foods sector, or improving individual and public health. The article concludes that the European Food Safety Authority may need to reconsider the epistemic policies hitherto adopted, by means of reviewing the prioritisation of its regulatory objectives and analysing the consequences for each level of proof in all contexts.