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This paper explores the influence of the Russian University Excellence Initiative (Project 5−100) on university governance structures. We conducted a qualitative study of the university, focusing on changes in academic and managerial self-governance. We found the following. First, the role of the administrators in university decision-making has been strengthened, especially the distribution of financial resources. Separate governing bodies were created from the central administration, the role of professional managers has become more prevalent in the Academic Council, and the tight control on academic departments was increased. These changes were brought about by the newly created role of rector, accompanied by new institutional capacities and financial resources. Second, although the university has called for the participation of academics in new initiatives, the formal governance structures remain relatively unchanged. Academics, including beneficiaries of the university transformation, have not gained greater formal decision-making power.