After the foiled Malvezzi conspiracy in 1488, Giovanni II Bentivoglio tightened his authority.
The tyrannical behaviour of the lord of the city thus became increasingly evident, yet he still managed to remain in power during the dangerous succession of incursions into Italy by the French, and the yearnings of the fearsome Cesare Borgia to take control of Romagna.
He was powerless, however, against the army of Pope Julius II, who,in 1506, regained possession of Bologna and acquired the loyalty of prominent local families by increasing their representatives in the Senate to forty but while effectively nullifying their authority, which was handed over entirely to the papal legate.
For its part, the Studium was fully supported by all the popes in the early 16th century, who decided not to change its hybrid nature as an entity run by private student guilds and public institutions.
The teachers were rewarded with an increase in salary and even had themselves proclaimed Aurati knights and Palatine counts, initially by Charles V, who came to Bologna to be crowned emperor in 1530, and then by Pope Paul III (1536), who could not be outdone.
Bologna had become the stage of Europe, where popes, sovereigns and their ambassadors would parade. They were hosted and entertained in the many modern palaces belonging to the wealthiest families.
Students and professors continued to arrive from all over, drawn by the last appeals of a university reputation that would soon fade away. They were also housed in the new national colleges located in the various districts of the city. (note or city map with the Colleges).
Among them, the following stand out for their importance: Erasmus of Rotterdam (1506), who was welcomed, for a short period, into the house of his professor and friend Paolo Bombace, a first-rate Greek scholar; Pietro Pomponazzi (1512-25) from Mantua, who was replaced by the teacher and rival Alessandro Achillini in the chair of Natural Philosophy; and the Swiss Paracelsus, who came to visit his teacher, the physician Jacopo Berengario da Carpi.
However, the internal and external approach of the Church suddenly changed mid-century, when Pope Paul III decided to bring the Council of Trent to Bologna in order to distance it from the imperial territories that had become hostile to the interests of Rome.
From 1547 onwards, Bologna became a bastion of the Counter-Reformation, and its University was also reorganised according to its strict principles.
The cardinal-legate became patron of the University, keeping the archdeacon of the cathedral under him as chancellor of the Studium.
They established a new supervisory body, the Assunteria (4 senators), which had economic and contractual powers that were often withdrawn from the Reformers of the Studium.
The College of Doctors was left with no other task than to examine undergraduates and new colleagues.
But those who really suffered were the students, who lost control of their Universitates (student guilds).
As part of the more complex modernisation project for the historic centre, Antonio Morandi, known as “Terribilia”, had built the first unified premises of Alma Mater Studiorum, which up to then had retained the medieval custom of holding its classes in teachers’ homes and in rented spaces in the city. The entire organisation could therefore be more easily controlled and the obligation to profess one’s faith more firmly imposed, which, in effect, forced many gifted Germanic students of the Protestant faith to leave the city and go to other universities.
The strict measures of the Counter-Reformation and the power of the Inquisition did not, however, have such negative effects as elsewhere, although two well-known expulsions remain in the city annals: that of the student Torquato Tasso, expelled in 1564 after spreading pungent satires on the respectability of certain professors and university colleagues; and that of the teacher Gerolamo Cardano, accused of heresy and forced to resign and leave the city in 1571.
The latter, along with Luca Pacioli, Scipione del Ferro, Niccolò Tartaglia and Lodovico Ferrari, was an absolute protagonist of modern Mathematics. Indeed, it was in Bologna that he found algebraic solutions to third- and fourth-degree equations and, subsequently, developed the new discipline of axonometry together with Bonaventura Cavalieri.
The Studium could also have excelled in Astronomy, but missed this opportunity, preferring the more modest Giovanni Antonio Magini to the young Galileo Galilei.
However, he was at the forefront and the first in Europe to create a chair of Natural Sciences (De simplicibus), tailored to the philosopher Ulisse Aldrovandi, who set up a special botanical garden for his research in the courtyard of the Apostolic Palace (now Palazzo Comunale) and organised the most comprehensive naturalistic classification ever made.
The faculty of Medicine was also greatly improved by the University in the 16th century. Still associated with Philosophy thanks to the distant Hippocratic example, respected for the first time in Bologna in the late 13th century by Taddeo Alderotti, the discipline remained bound to the theories of Aristotelian and Galenic works. However, an increasing knowledge of the secrets of the body could be acquired due to the practice of anatomical dissection. It was precisely in Bologna that the practice of autopsy was able to become a fully-fledged part of teaching activities thanks to Mondino de’ Liuzzi (14th century), although it met with great resistance from the Church. The latter, who had now become the disciplinary authority, not only accepted the practice but also encouraged it as a form of “training”, by creating a special anatomical theatre in the Archiginnasio Palace and encouraging students to attend the nearby Ospedale della Morte (Hospital of death). This allowed Surgery to merge with Medicine and led to the emergence of great names such as Leonardo Fioravanti and Gaspare Tagliacozzi.
The faculty of Law, instead, became rigidly criminalist (criminal law was established in Bologna in 1509), which was typical of Absolutist states, yet popes, cardinals and bishops were still allowed to graduate, including Ugo Boncompagni and Gabriele Paleotti, two canonists of Bologna who wrote the history of the post-Tridentine period, among other things.
They made 1582 a truly revolutionary year. Ugo Boncompagni, who had become Pope Gregory XIII ten years earlier, introduced the new calendar, which still bears his name, and succeeded in elevating his home town to a Metropolitan Archdiocese in the same year. Meanwhile, Gabriele Paleotti, the reformist cardinal, not only introduced major reforms for the reorganisation of the clergy and the moralisation of the Catholic doctrine, but also published the famous treatise entitled Discorso intorno alle immagini sacre e profane (Discourse on sacred and profane images), which all artists at that time were required to observe.
Among them were the three Carracci cousins who established their own academy, inaugurating a new season of European art in Bologna in 1582.