The central representative body of all Goethe University interest groups is the Senate. It consists of nine members from among the professorial staff, three students, three academic employees and two administrative-technical staff members.

The Executive Board is the university's managing body. It is made up of the President, four Vice Presidents and the Head of Administration. The president chairs the Executive Board and has the authority to issue guidelines. The president is elected by a majority of the elective assembly (Wahlversammlung), and acts as the university's external representative. The Head of Administration manages the university administration according to the Executive Board's guidelines and is responsible for the budget.

Being a Stiftungsuniversität, Goethe University is a university foundation under public law. In its Higher Education Act, the Federal State of Hessen places academic supervision within the hands of the university's governing bodies. The University Council, whose members come from outside Goethe University, and the Economic and Finance Committee, which is ultimately responsible for business matters, act as the university's supervisory body.

By returning to its original status as a university foundation under public law (Stiftungsuniversität) in 2008, Goethe University once more took up the Frankfurt foundation tradition. Following the reestablishment of the Stiftungsuniversität, the Foundation Board of Trustees was constituted on 19 May 2008.

The Committee of Faculty Deans is an internal advisory body consisting of all Faculty Deans as well as the members of the University's Executive Board.

The Deans of Studies' Committee was set up in 2010 to provide a forum for concerns related to teaching and to intensify the dialog between the Deans of Studies and the Executive Board. It is chaired by the Vice President for Studies, Teaching and Further Academic Education. The Deans of Studies' Committee meets up to four times a year. In addition to the Deans of Studies, other participants in the meetings include Dean's Office employees and representatives of the central units as well as of the AStA Students' Union Department for Study Conditions.

The Deans of Research Committee was set up as a forum at Goethe University in 2018, when, in July that year, the Research Deans or the Associate Deans responsible for research matters met for the first time to discuss relevant research topics with the Vice President for Young Talent, Research and Transfer. The Committee aims to intensify the strategic coordination between the university's management and the Faculties on research issues..

Established in 2021, the tasks of the Internal Advisory Board (IAB) include advising the University's Executive Board on the further development of the Profile Areas and, in connection with this, offering guidance for the submission of applications for collaborative projects as well as submitting nomination proposals for top-class research prizes and proposals for external experts (e.g. for evaluation procedures or expert activities). Its members were nominated by their Profile Areas and appointed by the Executive Board.