The faculty is organized as follows:
- Board. The department board sets out the course of the department.
- Research. The department of Applied physics has structured its research programs around a portfolio of research strengths. Research in these focus areas is conducted by small and flexible research groups. These groups contibute to national joint 'research school' efforts
- Education. The department offers bachelor- and master programs. For practicalities or details, please refer to the opleidingsinstituut.
- Employee participation is pushed forward by the faculteitsraad.
- Department staff. The department staff assists faculty and board in matters of HRM, Automatisation Groep Physics (AGN), communication, finance, logistics, health and safety, and policy making.