IBED is led by a Scientific Director, a role currently fulfilled by Prof. Annemarie van Wezel. The Scientific Director is given a wide-ranging mandate by the Dean of the Faculty of Science to run the Institute. She is responsible for the scientific programme and its quality, the contributions to the faculty's educational programme, and for human and financial resource management. As such the mandate includes the development of the scientific programme and profile of the institute, the financial planning and control, and the decisions concerning investments in facilities and instrumentation.
The actual day-to-day financial and personnel management is delegated to the Institute Manager, Monique van Wordragen, and her Management Office. She is responsible for the daily administrative processes, financial and personnel, and the shared facilities of the Institute. Together with the Director she oversees the yearly budget development of the Institute and works out the allocation of resources to the different research groups, facilities and labs. The Institute Manager also controls the income and expenditure of the Institute and makes assessments of the actual spending of research projects given the financial conditions set by the Institute and/or granting bodies.
In addition to the Director and the Institute Manager, the IBED Management Team (MT) consists of the Deputy Director (Merijn Kant) who is responsible for PhD portfolio, and Science Officer (Amber Heijboer), who is responible for internal and external PR of the institute's research and plays a supporting role in IBED's policy developments. The MT is supported by a Management Assistant of the IBED Office in the person of Saskia Heijboer.
The management board (MB) of IBED consists of the Management Team (MT) and the four heads of the research departments. The Science Officer acts as the secretary of the MB. These four Research Departments are Ecosystem and Landscape Dynamics (ELD), Evolutionary and Population Biology (EPB), Freshwater and Marine Ecology (FAME) and Theoretical and Computational Ecology (TCE).