He drew up special rules regarding the practice of religion, application to study, and conduct which each student bound himself by oath to observe.
Bishop Otto in 1563 gave the Jesuits, whose provincial at that time was Peter Canisius, charge of the instruction in the university, and authorized them to follow their own rules in all that pertained to organization and administration.
As, however, the cathedral chapter of Augsburg would not admit the legality of this complete transfer, disputes often arose on questions of right, especially in regard to episcopal visitation, the foundation of chairs of civil law, and the appointment of professors.
In 1641, Emperor Ferdinand III ratified the new charter in a special document which recognized the service rendered by the scientific work of the university and by the preparation which it gave young men for their duties toward Church and State.
During the Swedish invasion in the Thirty Years War the revenues of the university became less regular, some of its professors were imprisoned, its students scattered, and the lectures discontinued.
But after peace had been concluded the institution gradually recovered, and, in 1688, a building for university lectures was erected under Bishop John Christopher von Freyberg.
The university's charter guaranteed to all its members freedom from civil and political obligations, separate jurisdictions, and the right of precedenee on public occasions.
In 1610, Bishop Henry von Knöringen granted to the rector and the professors of theology the privilege of censorship; in 1747 this was modified to the effect that books printed in Dillingen needed also the approbation of the episcopal censor at Augsburg.
Although the frequent changing of professors was prejudicial to their literary activity, many of them acquired fame in the fields of moral theology, canon law, philosophy, mathematics, and astronomy.
Its students, 20-25 in number, were young men of parts, who, after completing the course of humanities and dialectics, pledged themselves to take their degrees at the university.
In 1582 the total number of students, including those in the gymnasium, was 600; in 1618 it was 306, and in the year of the suppression of the Society of Jesus, only 210 attended, of whom 116 were studying theology, 25 jurisprudence, 74 philosophy.
At first the number of students was nearly the same as formerly, but the institution soon began to labor under financial difficulties owing to the confiscation of lands and revenues which had belonged to the Jesuit college.
The endowments of several institutions and corporations were transferred in 1789 to the "Academic House" in order to relieve its financial difficulties, and its administration was simplified by uniting the St. Joseph Seminary and the convictus.
Hence it was several times proposed to transfer the university to a religious order, e.g. the Benedictines or the newly organized Societas de Fide Jesu.