The MOU is governed by a nine-member Board of Directors, which is appointed for a three-year term.

The company’s highest executive officer is the General Director.

The MOU headquarters are based in Athens and consist of the following departments:

• Legal Advisor
• Internal Audit Unit
• Unit for Methodology, Internal Audit Planning & Consulting Services
• Unit for Internal Audits
• Data Protection Officer (DPO)
• Quality Assurance
• Programming and Communication Unit
• Consulting and Support Services Department
• Expert Team for Remote and Island Areas
• Expert Team for Mountainous and Disadvantaged Areas
• Expert Team for Minority Groups and European Social Fund Projects 
• Expert Team for the Environment 
• Expert Team for State Aid Projects
• Human Resources Management Department
• Unit for Recruitment and Human Resources Management
• Unit for Training and Human Resources Development
• Information Technology Department
• Unit for Electronic Infrastructure and Networks Support
• Unit for Data Center & Cloud Computing Management and Support
  
• Internet Applications' Support Unit
• Unit for State Aid Information System Development and Support
• Expert Team for IT Applications of the Management Information System (MIS)
• Planning and Development Department
• Unit for Studies
• Finance and Administration Department
• Unit for Financial Management 
• Unit for Administrative Management 
• Unit for Technical Assistance Management 
• Procurement Department
• Procurement and Services Unit
• Infrastructure Development Unit
• Engineering Department
• Unit for Design Studies
• Unit for Special Projects' Studies
• Unit for Construction of Projects
• Secretariat