IAMO is made up of the board of trustees, the directorate and the scientific advisory board (see organigram). Along with representatives of the donors (the Federal Government and the state of Saxony-Anhalt) as well as the chairman and vice-chairman of the scientific advisory board, additional academic and public figures belong to the board of trustees. The board of trustees supervises the management of the institute, audits its economic management, approves the annual budget and provides support to IAMO's long-term research and development planning. Furthermore the board of trustees approves the activities of the executive board for the previous financial year.

The heads of the three academic departments and the head of the department for Administration and Central Services form the institute's directorate. In coordination with the board of trustees, this collegial body manages the institute's business and directs the long-term research, development and expansion planning of IAMO. This includes the compilation of research programmes and the responsibility for their realization, the formulation of proposals for filling management positions, the drawing up and the carrying out of the annual economic plan and the financial planning of several years, as well as the promotion of cooperation with universities and other research facilities.

The scientific advisory board advises the directorate and the board of trustees on academic and technical matters, supports connections with institutions dealing with the same scientific matters at home and abroad and carries out regular appraisal of the institute's work.