European Union agencies have been studied explicitly or implicitly from two distinct theoretical backgrounds: an intergovernmental and a supranational logic. The two logics relate to broader dynamics that aim to understand the forces that the EU responds to. Against this backdrop, the present paper asks the following question: how can intergovernmental and supranational perspectives be reconciled in the study of EU agencies? The question we put forward seeks to discuss EU agencies as singular artefacts that combine intergovernmental coordination and access to supranational power under conditions of institutional isolation and a strong professional identity. The paper problematizes the literature on EU agencies along these lines before proposing that these organizations be studied as part of broader dynamics linked to their coordinating role in European policy-making. We conclude with a plea to favor an analysis that would reconcile these two perspectives based on considering agencies as trans-governmental bodies operating in transnational spaces.