The GFCM is governed by its contracting parties and managed by an elected Bureau. Once a year it holds a statutory session where it adopts recommendations and resolutions as well as an annual work plan.  

To fulfil its mandate, the GFCM relies on advice from five subsidiary bodies responsible for providing advice on established priorities for Mediterranean and Black Sea fisheries and aquaculture, issues related to compliance as well as administrative and financial matters. Their work is in turn supported by technical working groups, ad-hoc workshops and strategic initiatives.  

The GFCM implements its policy and activities through its Secretariat and its sub-regional technical units.