This article studies and contextualizes the attempts to reform the University of Bologna in the decades around 1583. On the basis of little-known documents, it shows how Rome exploited a directive of university reform from the Council of Trent to gain increasing power over the running of the studio and also the city of Bologna. The request for a report by the Congregation of the Council in 1583, undertaken most likely at Gregory XIII’s request, laid the foundation for papal control, which was facilitated by overlapping and poorly defined lines of authority with respect to the university. Tensions internal to Bologna and the studio are also considered inasmuch as they affected the city’s relationship with Rome.