The EU integration process is caught between a phenomenon of supranational delegation from the Member States and autonomous constitutional developments. The comprehension of the agencification phenomenon in the EU internal market cannot be fully understood if the roles of the supranational polity and of the Member States are not distinguished in their contribution to supranational administration. This essay aims to investigate the legal legitimacy of EU agencies’ powers in the complexity of the European integration. By reconnecting the development of EU agencies to the composite nature of the EU as a Union of Member States, the essay shows that the development of EU agencies’ tasks responds to constitutional challenges embedded in the governance of the internal market. The analysis explains that the legitimacy process is more complex than the bottom-up approach of the supranational delegation and it relies on the development of the specific EU constitutional framework. The legitimacy questions shall therefore be addressed on broader grounds. Both the supranational delegation from the Member States and the constitutional autonomy of EU law contribute to understanding current accountability and legitimacy gaps in the functional design of EU agencies. On these grounds, only a more comprehensive public law paradigm can effectively contribute to understanding EU law and particularly the legitimacy of the exercise of administrative powers.