The Institute's organisation is clearly structured with management, Research Groups and the supporting service areas. The day-to-day management of the institute as well as the management of scientific agendas is the responsibility of the director, who appoints a management team to support him or her. This team includes two deputy directors, responsible for external and scientific affairs, who rotate from among the staff, and a financial and human resources manager. The Institute's Executive Board supervises WIFO's activities, for instance by approving the annual budget, convening the General Assembly, etc. The International Board advises WIFO on strategic issues and on the orientation of its research activities.

The economists and research assistants of the five Research Groups combine the expertise of economic subdisciplines as central organisational elements. Their work is characterised by the principles of strengthening scientific creativity and promoting personal responsibility and initiative. The research areas are supervised by rotating research area coordinators, who are responsible for resource and work planning.

The management and research divisions are supported by the divisions Research Service, Communication and Publishing, Business Cycle and Enterprise Surveys and Facility Management as well as the other WIFO service divisions Library, Event Management and the Data Science group.

The core instrument of WIFO's workflow organisation is the organisation of work in the form of projects in which flexible teams with clearly defined responsibilities and division of labour temporarily work together. Depending on the research question at hand, the project teams are also made up of people from different Research Groups and are temporarily headed by a project manager. For larger projects, a trained project manager is at his or her side who implements suitable instruments to ensure efficient project management and, if necessary, takes on organisational tasks.