EDA is the only EU Agency whose Steering Board meets at ministerial level. At the meetings of this governing body, Defence Ministers decide on the annual budget, the three year work programme and the annual work plan as well as on projectsprogrammes and new initiatives.

The Head of Agency, who is the High Representative of the Union for Foreign Affairs and Security Policy, is also Vice-President of the European Commission. The EDA Chief Executive is appointed by decision of the Steering Board. In addition to ministerial meetings at least twice a year, the Steering Board also meets at the level of National Armaments Directors, R&T Directors and Capability Directors.

Networks of national Points of Contacts (POCs) have an important role in the coordination of the Agency’s work with the Member States: Central POCs (for the preparation of the ministerial Steering Board as well as organisational, institutional and budgetary matters), Capability POCs, Research & Technology POCs and National Armaments Directors' POCs.

The European Defence Agency adheres to the key principles of good governance promoted by the European Ombudsman and has adopted internal policies and procedures to ensure a more accountable, transparent and ethical administration.