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There are four main components within the BSEC organizational structure:

• Intergovernmental (summits and sessions of the Council of Ministers of Foreign Affairs);
• Business (BSEC Business Council – coordination body for business initiatives);
• Financial (Black Sea Bank of Trade and Development);
• Academic (unified regional academic network of BSEC countries is being developed to be integrated with alike European networks).

Permanent bodies in the framework of BSEC activity.

Council of Ministers of Foreign Affairs - is the principal regular decision making organ of the BSEC. The Council’s terms of reference cover the following:

• decision making on all issues pertaining to the functioning of the BSEC;
• considering all matters submitted by the Subsidiary Organs;
• decision making on membership and status of observer and sectoral dialogue partner; 
• establishing Subsidiary Organs within the BSEC, assigning tasks to them;
• considering any other related matters it may deem appropriate.

Committee of Senior Officials representing the Ministers of Foreign Affairs of the Member States and acting on their behalf, is entrusted with the following competencies:

• reviews activities of the Subsidiary Organs, evaluates the implementation of decisions and recommendations of the Council and elaborates recommendations and proposals to be presented to the Council;
• considers issues related to coordination and cooperation with BSEC related bodies, informs the Council about these issues and works out, if necessary, pertinent recommendations and proposals;
• studies organizational aspects of the BSEC activities, participates in the elaboration of preliminary calendar of events;
• submits to the Council for approval the annual budget of the BSEC;
• nominates experts to a specialized sub-group for carrying out the budget auditing.

Parliamentary Assembly of the Black Sea Economic Cooperation (PABSEC) represents national Parliaments of the Member States, provides consistent support to the Black Sea cooperation process on a consultative basis.

Black Sea Trade and Development Bank – international financial organization. The purpose of the Bank shall be to effectively contribute to the transition process of the Member States towards the economic prosperity of the people of the region and to finance and promote regional projects and provide other banking services to projects of the public and private sectors in the Member States.

BSEC Business Council is an international non-governmental organization, consists of representatives of the business communities of the BSEC Member States.

Permanent International Secretariat (PERMIS) is located in Istanbul, Republic of Turkey. The PERMIS is functioning under the authority of the Chairman-in-office of the BSEC, that is performed through Secretary General.

Chairman-in-office - the Minister of Foreign Affairs of the Member State which assumes the Sessional Chairmanship of the BSEC or any other Minister designated for this purpose by the Government of State in question. The Chairmanship shall rotate every six months according to the English alphabetical order. Should the Chairmanship be waived by a Member State, it will be assumed by the next Member State in line.

Troika System is the system which consists of the Chairman-in-Office, the previous and the next Chairman of the BSEC or their representatives. Upon request of the Chairman-in-office, the Troika convenes at the appropriate level in order to exchange views on current and prospective activities of the BSEC and on its relations with other international organizations and institutions.

Subsidiary Organs - any Working Group, Group of Experts, Task Force, Committee or service established by the Council of the Ministers of Foreign Affairs or under its authority. The Subsidiary Organs shall carry out their mandate defined by the Council as well as pursuing the implementation of such projects/activities in their respective areas.

BSEC affiliated centers are established upon approval of the Council to serve all the interested Member States on specific areas of cooperation. The results of the centers' activities are of consultative nature.