The Faculty of Law was awarded the honour of a count palatine for its dean. This entitled it to audit and appoint notaries (until the Imperial Justice Reform of 1879).

The Faculty of Artists, which had been teaching the seven liberal arts (the trivium - grammar, arithmetic, geometry; and quadrivium - music, astronomy, dialectics, rhetoric) as well as the Latin language, took on new tasks as the study of the natural sciences developed, and entered the ranks of the upper faculties, becoming the Faculty of Philosophy.

In 1573 and 1584, the strengthening sovereignty of the state led to “inheritance settlements” with the city of Rostock, as a result of which the University was able to strive for peaceful upward development. It achieved supra-regional importance, and the influx of students grew.

_{Source: 575 Jahre Universität Rostock. Mögen viele Lehrmeinungen um die eine Wahrheit ringen. Rostock 1994, S. 327-328.}

_{Further reading:
550 Jahre Theologie an der Rostocker Universität. Vorträge und Grußworte der Festveranstaltungen anläßlich des 550. Jahrestages der Gründung einer Theologischen Fakultät an der Universität Rostock, hg. von der Wilhelm-Pieck-Universität Rostock. Sektion Theologie, [Rostock] 1983.}

_{Asche, Matthias: Von der reichen hansischen Bürgeruniversität zur armen mecklenburgischen Landeshochschule. Das regionale und soziale Besucherprofil der Universitäten Rostock und Bützow in der Frühen Neuzeit (1500-1800). Stuttgart 2000 (Contubernium, Bd. 52).}

_{Beiträge zur Geschichte der Juristischen Fakultät der Universität Rostock. Materialien eines im Sommersemester 1994 aus Anlaß des 575jährigen Jubiläums veranstalteten Seminars. Rostock 1994.}

_{Boeck, Gisela; Lammel, Hans Uwe; Münch, Ernst; Wagner, Wolfgang E.: Vom Collegium zum Campus. Orte Rostocker Universitäts- und Wissenschaftsgeschichte. Rostock 2007.}

_{Koppmann, Karl: Die Rektoren der Universität und die Dekane der artistischen Fakultät von 1563–1608. In: Beiträge zur Geschichte der Stadt Rostock 3.4 (1903), S. 45-64.}

_{Speicher des Wissens. 444 Jahre Universitätsbibliothek Rostock (Traditio et Innovatio, Sonderausgabe 2013).}

From 12-16 November 1619, celebrations to mark the end of the second century of the University's existence were held. The brilliant success of its resurrection following the Reformation was emphasised.

The University celebrated the centenary of the Augsburg Confession, unhindered by the Catholic occupation. The theologian Johannes Klein gave a forceful speech against the papacy.

When the city commander was murdered under academic jurisdiction by a non-university associate, the autonomous University, being approved by the Pope and confirmed by the Emperor, remained unchallenged.

The secularisation was confirmed in the peace Treaty of Münster, and the diocese of Schwerin was dissolved. Thus, the chancellorship was transferred to the respective bishop, and supreme supervision of the University was transferred to the ruling sovereigns, who maintained and exercised this power until 1918.

The house of the former “Wasserkunst” on the Grube was given to the University for astronomical purposes (until 1760).

_{Source: 575 Jahre Universität Rostock. Mögen viele Lehrmeinungen um die eine Wahrheit ringen. Rostock 1994, S. 328-329.}

_{Further reading:
Brodkorb, Clemens: Bistum Schwerin. In: Gatz, Erwin (Hg.): Die Bistümer des Heiligen Römischen Reiches von ihren Anfängen bis zur Säkularisation. Freiburg 2003, S. 670-675.}

_{Jakubowski, Peter: Joachim Jungius und der erste Höhepunkt in der Naturerkenntnis an der Rostocker Universität. In: Wissenschaftliche Zeitschrift der Universität Rostock, Bd. 35 (1986), 9, S. 64-69.}

_{Krabbe, Otto Carsten: Aus dem kirchlichen und wissenschaftlichen Leben Rostocks. Zur Geschichte Wallensteins und des Dreissigjährigen Krieges. Berlin 1863.}

The University lost its law school in the Alter Markt as the result of a major fire in Rostock, which destroyed 700 houses. The Rector, the physician Johannes Bacmeister, lost his house and all its contents, along with all the documents of the Faculty of Medicine stored in the house - an irreplaceable loss for medical history research on the history of the Faculty.

At the beginning of the 18th century, the University saw a modest flourish, but had the image of a small state university of average level, as was the case with other universities of the same size.

In the spring of 1702, Duke Friedrich Wilhelm moved his residence from Schwerin to Rostock and, with his colleges, took over almost the entire university building, the White College, the University itself having to make do just with the ground floor. Even when the Duke had to return to Schwerin two years later, the rooms being used were not released. In addition to disputes with the city council, there were now spatial difficulties.

On the occasion of the intended celebration of the University's three hundredth anniversary, Duke Karl Leopold announced that this could not take place because of the unrest in the state and would have to be postponed. But even in 1720 the time was not right for a worthy secular celebration, and the celebration still did not take place. Duke Karl Leopold tried every means to transform Mecklenburg into a state with absolute governance and to make the city of Rostock a royal seat. He wanted to eliminate or restrict the superior position of the estates. At the instigation of the knighthood, however, the Imperial Court Council withdrew the power of governance from the Duke and appointed his brother Christian Ludwig as administrator. These so-called “Mecklenburg troubles” formed no basis for prosperous work at the University.

Through skilful politics, Duke Christian Ludwig manage to make the city council concede and, on 20 April 1748, a corresponding settlement was concluded. On 18 April 1755, however, the Duke was forced to sign the notorious “Landesgrundgesetzlichen Erbvergleich” (Basic Law on Inheritance Settlement) - the Magna Carta of the Mecklenburg estates. The settlement constitutionally determined the relationship of the sovereignty with the estates, including Rostock. The settlement act blocked any progressive constitutional development in Mecklenburg.

_{Source: 575 Jahre Universität Rostock. Mögen viele Lehrmeinungen um die eine Wahrheit ringen. Rostock 1994, S. 329-331.}

_{Further reading:
Asche, Matthias: Bildungsbeziehungen der Hansestadt Lübeck zur Universität Rostock vom 15. bis zum 18. Jahrhundert. Chronik eines regen kulturellen Austausches auf den Spuren der Hanse. In: Lübeckische Blätter, Bd. 164 (1999), 15, S. 221-225.}

_{Kohfeldt, Gustav: Rostocker Professoren und Studenten im 18. Jahrhundert. Schilderungen nach den Akten und nach zeitgenössischen Berichten. Rostock 1919.}

_{Koppmann, Karl: Rostocks Stellung in der Hanse. In: Mecklenburgische Jahrbücher, Bd. 52 (1887), S. 183-208.}

_{Manke, Matthias: Verfassung und Lebenswirklichkeit. Der Landesgrundgesetzliche Erbvergleich von 1755 in seiner Zeit. Lübeck 2006.}

_{Raabe, Wilhelm: Carl Leopold, aus Schwerin vertrieben, residirt in Wismar und Dömitz. In: Raabe, Wilhelm: Specielle Landes- und Volkskunde beider Großherzogthümer, Wismar 1863, S. 1033-1042.}

_{Ziegler, Uwe: Die Hanse. Aufstieg, Blütezeit und Niedergang der ersten europäischen Wirtschaftsgemeinschaft. Eine Kulturgeschichte von Handel und Wandel zwischen 13. und 17. Jahrhundert. Bern 1996.}

Teaching in Rostock began on 28 April 1789. The rooms in the university building being used for the purposes of the state government were vacated. To accommodate the Justice Chancellery housed in the White College, the University had to give up the building in Langen Strasse. This was later replaced by a new building for Rostock Higher Regional Court.
The term of office for rectors and deans - previously one semester - was set at one year.
On 4 December 1789, the Duke appointed Adolph Friedrich Loccenius, Director of the Chancellery involved in the negotiations for the merger, as the first Vice-Chancellor (Curator) of the University, who, as the state supervisory officer, was to supervise all processes at the University in addition to the fixed individual tasks.
Loccenius was eager, but less than successful, in fulfilling his mission. When he died on 2 July 1793, no successor was appointed.

The Faculty of Law building in the Alter Markt, which was destroyed in the fire of 1677, was converted into the Anatomical Institute of the Faculty of Medicine. So it was that the Faculty received its first dedicated building on 3/11/1790.

Franz Christian Lorenz Karsten, Professor of Economics (Agriculture, in Bützow 1775-1789 and in Rostock 1789-1828), was one of the first people in Germany to give lectures on agriculture. He set up a small agricultural experimental station for the practical training of students. However, there was no financial support from the State or the University.

Establishment of the Theological Pedagogical Seminar.

_{Source: 575 Jahre Universität Rostock. Mögen viele Lehrmeinungen um die eine Wahrheit ringen. Rostock 1994, S. 331-332.}

_{Further reading:
Asche, Matthias: Die mecklenburgische Hochschule Bützow (1760-1789) - nur ein Kuriosum der deutschen Universitätsgeschichte? Versuch einer historischen Neubewertung. In: Jahrbuch für Universitätsgeschichte, Bd. 9 (2006), S. 133-147.}

_{Camenz, Günter: Zur Geschichte der Universität "Fridericiana" in Bützow 1760-1789. Bützow 1999.}

_{Hölscher, Uvo: Urkundliche Geschichte der Friedrichs-Universität Bützow. In: Mecklenburgische Jahrbücher, Bd. 50 (1885), S. 1-110.}

_{Velthusen, Johann Kaspar: Nachricht von der Stiftung eines Herzoglichen pädagogisch theologischen Seminariums auf der Universität Rostock. Rostock 1790.}

_{Wegner, Christoph: Franz Christian Lorenz Karsten. Eine kritische Biographie. In: Buchsteiner, Martin (Hg.): Zur Entstehung der Agrarwissenschaft. Beiträge zu Leben und Werk von Franz Christian Lorenz Karsten und Johann Nepomuk Hubert (von) Schwerz. Norderstedt 2010, S. 55-111.}

_{Wegner, Richard N.: Zur Geschichte der anatomischen Forschung an der Universität Rostock. Wiesbaden 1917.}

The Napoleonic Wars diverted attention. French troops occupied the whole country in 1806. The University had to hand over the Anatomical Institute in the Alter Markt to the French occupying forces, as well as the Auditorium Magnum, which was first used as a military hospital, and later as a recruiting depot.

In 1812, the Convictoria building in the Johannis-Kloster was confiscated for military purposes. After their defeat in Russia, the French troops withdrew, and Russian troops occupied Mecklenburg. The Duke lifted the Napoleonic Continental Blockade and announced the dissolution of the Confederation of the Rhine. Students registered as volunteers, and lectures at the University were interrupted.

After Napoleon’s defeat at Leipzig (16/10/1813), the University returned to settled work again.

During the Wars of Liberation, the idea of German unity was awakened among the students. In 1815, a unified fraternity was founded in Jena, followed by the “Rostochia”, founded in Rostock in 1812. The activities of the fraternity drew the attention of the governments of the countries of the “German Confederation” and hinted at “signs of imminent revolution”.

The building of the Anatomical Institute in the Alter Markt, which was used as a military hospital by the Napoleonic troops, was not taken back into operation until 1818, following necessary repairs, thus giving the medical students a place for practical training.

_{Source: 575 Jahre Universität Rostock. Mögen viele Lehrmeinungen um die eine Wahrheit ringen. Rostock 1994, S. 333-334.}

_{Further reading:
Höffer, Volker: Das studentische Verbindungswesen an der Universität Rostock vom Ausgang des 18. Jahrhunderts bis zum Vorabend der bürgerlich-demokratischen Revolution in Deutschland. Rostock 1987.}

_{Hoppe, Klaus-Dieter; Nenz, Cornelia; Weiß, Detlef (Hg.): Franzosenzeit in Mecklenburg. Begleitkatalog zur ständigen Ausstellung "Franzosenzeit in Mecklenburg" des Fritz-Reuter-Literaturmuseums im Gewölbe des Stavenhagener Schlosses. Rostock 2007.}

_{Manke, Matthias; Münch, Ernst (Hg.): Unter Napoleons Adler. Mecklenburg in der Franzosenzeit. Lübeck 2009.}

_{Reincke-Bloch, Hermann: Mecklenburg zu Beginn der Freiheitskriege. Rede gehalten in der Aula der Universität am 28. Februar 1913 bei der akademischen Feier zur Erinnerung an die Befreiungskriege. Rostock 1913.}

On 16 September 1820, Legation Councillor von Schmidt was dismissed from the position of government representative; on 12 October 1820, the Deputy Director of the Rostock Justice Chancellery, Karl Friedrich von Both, was entrusted with this position. In 1836, he was also appointed Vice-Chancellor (Curator) of the University, and over a 50-year term he earned credit for the University and its preservation. (Ducal Instructions for von Both)

_{Source: 575 Jahre Universität Rostock. Mögen viele Lehrmeinungen um die eine Wahrheit ringen. Rostock 1994, S. 334-335.}

_{Further reading:}

_{Büssem, Eberhard: Die Karlsbader Beschlüsse von 1819. Die endgültige Stabilisierung der restaurativen Politik im Deutschen Bund nach dem Wiener Kongreß von 1814/15. Hildesheim 1974.}

_{Grotefend, Hermann: Zur Geschichte der Rostocker Burschenschaft. In: Mecklenburgische Jahrbücher, Bd. 84 (1919), S. 123-130.}

_{Koppmann, Karl: Zur Geschichte des Blücher-Denkmals in Rostock. [Rostock] 1909.}

_{Kurth, Alexandra: Männer - Bünde - Rituale. Studentenverbindungen seit 1800. Frankfurt am Main u.a. 2004.}

_{Schmidt, Martin H.: Das Blücher-Denkmal in Rostock von Johann Gottfried Schadow. In: Gebhard Leberecht von Blücher und seine Zeit. [zum 250. Geburtstag], [Red. Wolf Karge]. Rostock 1992, S. 19-42.}

When Professor Heinrich Spitta came to Rostock in 1825, he succeeded in obtaining permission from the city's Armenkollegium to run an outpatient clinic with the participation of the students in the Municipal Hospital in Grubenstrasse.

The Government Plenipotentiary was instructed to audit all funds and associated records, the proper use of the funds and their secure allocation. There was no objection on behalf of the University. The first step for the state government to exert influence on the financial administration of the University was taken.

Source: 575 Jahre Universität Rostock. Mögen viele Lehrmeinungen um die eine Wahrheit ringen. Rostock 1994, S. 335-336.

_{Further reading:
Hückstädt, Arnold: Fritz Reuter und die "Allgemeinheit", John Brinckman und die "Gesellschaft der Volksfreunde". Rostocker Studentenverbindungen zwischen 1831 und 1834. In: Brunners, Christian (Hg.): Fritz Reuter, John Brinckman, Dethloff Carl Hinstorff und Rostock. Rostock 2002, S. 8-24.}

_{Jügelt, Karl-Heinz: Bibliotheca Philosophica - Bibliotheca Academica - Universitätsbibliothek. Bücher, Bibliothekare und Ereignisse in der 425jährigen Geschichte der Universitätsbibliothek Rostock. In: Mögen viele Lehrmeinungen um die eine Wahrheit ringen. Hrsg. vom Rektor der Universität Rostock. Rostock 1994, S. 40-69.}