The organizational structure of the MPI-CBG is as follows: There is a flat structure without departments, but about  twenty five Research Group Leaders (RGLs) who are fully independent and not tied to a particular Director or Department. The five research directors are also considered RGLs.

Matters of general interest to the institute are brought to the Faculty for information and discussion by different bodies and committees. So the main function of the Faculty is to keep everyone informed and connected. The Faculty consists of the directors, RGLs, Service and Facility Leaders (SFLs), a representative from Administration (Chief Operating Officer), from the postdoctoral program and from the PhD/pre-doctoral program.

Thus, the structure of the institute is kept at a minimum of hierarchy. Continuity is provided by the directors, while the turnover of most other scientific staff gives the necessary flexibility to constantly bring new expertise and ideas to the institute.

The budget is distributed directly between the Directors and the Research Group Leaders. Additionally, MPI-CBG has established services and facilities, which constitute the centralized scientific research infrastructure and allow researchers shared access to sophisticated and expensive technologies that would be hard or impossible for the institute to provide to each research group individually. The services and facilities are independent of the Directors and the Research Group Leaders and are financed by recharging the user, a model that has worked very successfully because it makes the services and facilities accountable to the research groups and ensures that they serve the researchers' needs and keep high quality standards.