Current debates on the future of the European Union tend to privilege statist perspectives according to which geopolitical challenges and internal politicization either spur disintegration, or drive the EU towards more federalist, centralized and externally bounded features. Starting from the EU's multilevel and polycentric architecture, this article investigates how far such federalist dynamics reach out to task-specific, functionalist EU institutions, such as regulatory agencies. Enjoying a certain degree of autonomy from the EU's central, politically encompassing institutions, regulatory agencies have established close ties with third country regulators to tackle interdependence. Based on the comparative analysis of six regulatory agencies representing varying patterns of international interdependence, sectoral politicization and regulatory authority, we show that functionalist pressure for international cooperation indeed sustains fluid boundaries. However, EU central institutions such as the Commission and the Parliament have increasingly claimed control over agencies' external ramifications. The result is enduring functionalist de-bordering, but federally controlled.