Research at IRD is organised into joint research units, international joint units and joint support units in five scientific departments.

Joint units report to an IRD regional delegation (geographical) and are scientifically accountable to one or more IRD scientific departments.

The organisation of its research also includes other research units such as JEAIs (young teams associated with IRD) and international joint laboratories, designed to foster the development of sustainable and autonomous Southern research teams. More recently, the creation of GDRI-Sud Southern international research groups has been added to this structure.