IGB has a matrix structure with disciplinary-oriented 6 Research Departments and 3 cross-cutting Research Domains ("Programmbereiche") that effectively integrate research activities across departemental boundaries. Each Department Head holds a joined professorship with one of the three universities in Berlin. The present cross-cutting Research Domains are coordinated by a Coordinator, a leading scientist at the institute.

The principal decision making body at IGB is the Board of Directors ("Leitungsgremium"). The Scientific Director ( at present: Prof. Dr. Mark Gessner), the Administrative Head (the Head of the Forschungsverbund Berlin e.V., at present: Dr. Manuela Urban) and the Department Heads have voting rights.

The Scientific Advisory Board supports the Board of Directors in improving existing and initiating new research directions.