AIE is governed by two main bodies, the General Assembly and the Executive Committee, they are responsible for the decision-making of the organization. The General Assembly is the highest authority of the organization, composed by all members, responsible for the political impetus and strategic orientations.
The Adriatic Ionian Euroregion has also the President who is the legal representative and manages the AIE in accordance with the decisions of the Assembly. There are also two Vice-President nominated by the Assembly to support the President.
The Thematic Commissions handle all thematic policies relevant for the network, while the AIE Secretariat is made up of one Secretary General and a team of dedicated people working to facilitate interactions between the members and to inform them of all the relevant news and activities.
According with the statute the association has the following bodies:
- Executive Committee
- Supervisory Board