The IODE Secretariat is responsible for the day-to-day management of the IODE Programme. Since 2005, it has been based at the IOC Project Office for IODE, Oostende, Belgium, hosted by the Flanders Marine Institute through funding provided by the Government of Flanders (Kingdom of Belgium). The Oostende office also hosts the IOC Capacity Development coordination unit (since 2017).

The Secretariat has 9 staff members in Oostende and several around the globe (Cayman Islands, South Africa, Mallorca, Canada, Australia, …).

The IOC Capacity Development (CD) unit (also hosted in Oostende by the IOC Project Office for IODE)is headed by the head of the IOC Project Office for IODE, has a staff member based in the Philippines.