The Board is composed of representatives from Member State and the European Commission. The latter chairs the Board and is also in charge of the Board's Secretariat. The Committee of the Regions, the EU Cybersecurity Agency and the European Cybersecurity Competence Centre participate as observers.

The Board meets twice a year. The Steering Board is responsible for preparing the agendas and meeting documents of the Board. The Steering Board is composed of the Chair of the Interoperable Europe Board, up to two elected Member State representatives, and one representative from each of the Member States of the current Trio Presidency of the Council of the European Union.

Each year, the Board adopts its work programme prepared by the Steering Board. The work programme outlines the main areas of focus and provides a preliminary calendar and agendas for the upcoming Board meetings.

The Board may set up working groups to prepare the work of the Board. The former Expert Group on interoperability of European public services has been transformed into a permanent working group of the Board, tasked with following up on the Board's decisions and assisting with the operational preparations of its discussions.

Other working groups may be established to enable deeper discussions among experts on specific topics. Besides Member State representatives, future working groups may also involve members of the Interoperable Europe Community.

The Interoperable Europe Community, established by the Interoperable Europe Act, helps to channel feedback, user and operational needs, as well as to identify areas for further development and help scope priorities for EU interoperability cooperation.

The Board may, when needed, consult the Community and seek for its advice and expertise in all matters related to cross-border interoperability.

The annual online Assembly brings together the Interoperable Europe Community, providing a venue for sharing of experiences and discussing policy and practical dimensions related to cross-border interoperability.

Every EU Member State has to designate national competent authorities and a single point of contact who is responsible for the application of the Interoperable Europe Act by 12 January 2025. 

Also, Union entities that regulate, provide or manage trans-European digital public services have to designate an interoperability coordinator to ensure the implementation of the Regulation.