Part of the Programme structure is how and by whom the Programme is managed. The managing structure comprises the following Programme bodies:
- A joint Monitoring Committee, including representatives of all eleven countries, selects projects for funding, oversees the overall implementation and is responsible for the correct use of the funds.
- The Investitionsbank Schleswig-Holstein (IB.SH) acts as the Managing Authority and Certifying Authority and concludes subsidy contracts with project lead partners.
- The Joint Secretariat is the focal point for information and practical day-to-day implementation. It is located in Rostock, Germany and Riga, Latvia.
- The Audit Authority verifies the effective functioning of the management and control system of the programme and ensures sample audits of projects. It is hosted by the Ministry of Justice, Cultural and European Affairs of the German Federal State of Schleswig-Holstein at Kiel, Germany. The Audit Authority is assisted by the Group of Auditors comprising representatives of the participating countries carrying out the second level audits.
Besides these Programme bodies national sub-committees play an important role regarding the dissemination of information in the participating countries.
Project lead partners, project partners and their first level controllers complement the managing structure in the overall Programme structure on the project level.
The following chart illustrates the Programme structure.
The participating countries have agreed on this joint programme management structure. To stipulate its set-up the countries signed an “Agreement on the Management, Financial and Control Systems of Interreg Baltic Sea Region, Programme period 2014-2020” with the IB.SH, the appointed Managing and Certifying Authority and operator of the Joint Secretariat of the Programme.
The participating countries also agreed to open the Programme to partners from outside the Programme area provided that any such country on whose territory the specific partners are located accepts the provisions for management, financing and control of the Programme. Signing the "Agreement on Management, Control and Audit concerning beneficiaries located outside the Programme area of the Interreg Baltic Sea Region Programme 2014-2020" by the specific country is obligatory before a payment from the Programme can be made to these partners. Guidance on how to include partners from outside the Programme area is provided in the Programme Manual and specifically for each call for projects.