However, the importance of the Studium was fully recognized with a Bull by Popo Clemente VI in 1349, in which he officially authorised the Studium to grant regular degrees, extended the Privilegia maxima, and established that the first Italian Faculty of Theology would be in Florence.

In 1364, with Emperor Carlo VII, the Florentine Studium became an Imperial University. However, when Lorenzo the Magnificent gained control of Florence and much of Tuscany, the Studium was moved to Pisa, in 1473. Carlo VIII moved it back to Florence from 1497-1515, but with the return of the Medici family it was once again transferred to Pisa.

In spite of these moves, many teaching activities continued in Florence, and scientific research found substantial support in the various Academies of the time, like the Crusca and the Cimento.

Only in 1859, when the Grand Duke was exiled, were all these separate teaching activities reunited in a suitable system called the Istituto di Studi Pratici e di Perfezionamento; a year later this was recognized as a full fledged university by the Government of Unified Italy.

In 1923, with a special Act of Parliament the Instututo was officially denominated a University.
Later, the new University was organized into the various faculties: Agriculture, Architecture, Arts, Economics, Education, Law, Mathematics, Physical and Natural Sciences, Medicine and Surgery, Pharmacy, and Political Science. The Faculty of Engineering, where 2-year courses had been offered since 1928, was added to the 10 faculties in 1970.