This EGTC has a multilevel governance with 4 levels:
- States
- Regions
- provincial level
- Intermunicipal organisations (links with municipalities and civil society)
The EGCT has one President and three vice-presidents. The Executive Management Committee consisting of 32 members and it is the executive body of the EGTC. The Assembly is composed of 84 members.
The Cross-Border Agency is responsible for six permanent thematic working groups.