EU agencies have become key actors in the operationalization of the EU regime on public access to documents. A tension between confidentiality and transparency has become particularly evident in the framework of regulatory procedures concerning chemical substances, food, and medicinal products. Applicants must provide EU agencies with commercially sensitive information to trigger the scientific and technical evaluation needed for marketing authorization or approval. We analyse three EU agencies: European Chemicals Agency, European Food Safety Agency, and European Medicines Agency. They hold information that is both commercially sensitive and highly relevant for EU regulators and the public at large. Using decisions of the EU courts and the European Ombudsman, this article shows how a new “ownership” paradigm seems to have evolved, in conflict with EU public access legislation. New rulings on the Aarhus regime suggest that more information should in the future become disclosable, putting the agencies under increased pressure by companies trying to protect industry know-how. EU agencies are constantly arbitrating between conflicting public interests. As the exercise of political discretion is exactly what EU agencies are not expected to do, the situation calls for legislative intervention.