The governance and structure of the Bonavero Institute is governed in terms of a Constitution approved by the Law Board and the Board of the Division of Social Sciences within the University. The Director of the Institute reports to the Dean of the Faculty of Law and to a Management Committee, established in terms of the Constitution, which meets termly. It is chaired by Professor Liz Fisher, a member of the Faculty of Law and a fellow of Corpus Christi College.

The Bonavero Institute has an Advisory Council to provide strategic advice and guidance. Members include human rights scholars and practitioners from across the world, including senior judges from the UK and human rights lawyers from Colombia, Germany, India, Mexico, South Africa, and the United States. The Advisory Council meets once a year to review the annual report of the Bonavero Institute and to discuss plans for the next year. In addition, Advisory Council members support the Bonavero in many other ways, such as delivering lectures or presentations, providing advice on aspects of our research work, and supporting our programmes. Advisory Council members serve for renewable terms of three years.