This article analyzes the debate about data acquisition and assessment in health claims regulation by identifying the underlying controversies on methodological choice. Regulation in the European Union imposes the need for a scientific substantiation of all health claims (claims about a relationship between consumption of certain food ingredients and positive health effects). Randomized controlled trials (RCTs) are the method that generally is considered to provide the highest quality data for decision making in claims regulation because they allow for establishing cause–effect relationships. The latter are demanded in European regulatory practice for authorization of a claim. This requirement has contributed to a debate about the advantages and limitations of the RCT methodology in nutrition research and regulation. Our analysis identifies five types of tensions that underlie the controversy, with respect to evidence, cognitive values, standards of proof, future lines of research, as well as expert judgment. We conclude that there is a direct and mutual interaction between methodological decisions in nutrition science, and different strategies in health claims regulation. The latter have social and public health consequences because not only may they affect the European market for functional foods, as well as concomitant consumption patterns, but also the generation of future regulation‐relevant evidence in nutrition.