The organizational structure of Fraunhofer ISE is defined, apart from Directorship, Administration and Communications by the scientific divisions Photovoltaics and Energy Technologies and Systems, their departments, groups and teams, as well as the department Electrical Energy Storage.

Five market-oriented business areas are used for external representation Photovoltaics, Energy Efficient Buildings, Hydrogen Technologies and Electrical Energy Storage, Solar Thermal Power Plants and Industrial Processes and Power Electronics, Grids and Smart Systems