Recent research has paid increasing attention to the institutional dynamics of EU agencies in post-delegation but has barely explored the conditions under which patterns of informality shifting institutional power balances are likely to emerge on agency boards. Based on documentary analysis and 60 semi-structured interviews covering 22 agencies, this article examines under what conditions boards’ formal configurations in which the Member States hold a majority are informally altered to the advantage of the Commission. The article argues that functional motivations are present in the emergence of informal rules empowering the Commission, but those rationales are conditional to distributional considerations.