16th century

1504	December 19: Konrad Stein from Jena, canon of Erfurt, donates the Maria Magdalene Chapel in front of the barrel mill near the hospital to accommodate pilgrims.
1506	With the completion of the vaulting work on the nave, the building work on the town church of St. Michael is essentially finished, with the exception of the tower construction.
1509	July 30: The inn "vor dem Lobderthore", predecessor of the "Roter Hirsch" ("Zum Roten Hirsch"), is mentioned.
1511	The order of St. Michael's Monastery lists a total of 16 altars in the church of St. Michael.
1518	A foreign monk repairs the organ in the town church.
1521	June 15: Thomas Müntzer writes to the Jena city judge and councillor Michael Ganßau, indicating Müntzer's influence on the early Reformation movement in Jena . December 24/25: Martin Reinhart, preacher at the town church, serves communion in both forms to three citizens at Christmas, which can be seen as the first indication that the Reformation is underway.
1522	March 4/5: Martin Luther spends the night at the "Schwarzer Bär" inn as Junker Jörg on his journey from Wartburg Castle to Wittenberg. August: Reinhart and his followers invade the Dominican monastery. Further violent actions against the Jena monasteries follow.
1523	The Reformation in Jena is shaped by the radical movement represented by Andreas Karlstadt, who worked as a priest in Orlamünde , especially by his student Reinhart. Michael Buchführer, who worked in Jena in 1523/24 , printed writings by Karlstadt and his followers, bypassing the censors .
1524	August 20: The council confiscates the property of the Carmelite monks and has it transferred to the town hall. August 22: Luther preaches in St. Michael's against Karlstadt and his followers and then argues with Karlstadt in the "Black Bear". September/October: Karlstadt and Reinhart are expelled from the country. As a newly appointed preacher in Jena, Anton Musa continues the Reformation in Luther's spirit.
1525	April 30: Insurgent peasants and townspeople plunder the manors near Drackendorf and Lobeda. May 3: The Carmelite monastery in Jena, followed a few days later by the Dominican monastery, is stormed, robbed and partially destroyed. Both monasteries remain closed after the end of the uprising. The Cistercian nunnery, which was spared by the insurgents, serves as a refuge for the few remaining nuns until the death of the last of them in 1564, but is no longer allowed to accept new nuns. June 22: During Elector Johann's punitive campaign against the rebellious peasants, twenty rebels from Jena and the surrounding area are said to have been executed by the sword on the Jena market. December: The city council and St. Michael's Monastery conclude an agreement under which the appointment of pastors and the external organization of pastoral care become a matter for the city.
1526	The establishment of a "common fund" to pay the clergy and for the general financing of the new church and school system as well as the care of the poor begins. Subsequently, parts of the previous monastery income or sold monastery property are allocated to it.
1527	The visitations of the church ordered by the sovereign finally enforce the Reformation in the villages around Jena. August 17: Anton Musa is officially appointed parish priest of Jena, an office he holds until 1536. At the same time, he is appointed superintendent for Jena, Bürgel and Eisenberg.
from 1529	The school system is reorganized and the schoolhouse is set up in the former nuns' house behind the town church. A girls' school, in which elementary knowledge of writing, religion and "female handicrafts" is taught, is documented for the first time.
1534	Construction of the "Fürstenkeller" begins. The huge vaulted cellar is initially used to store the wine to which the sovereigns are entitled as a tax. May 24: The first public shooting of birds takes place at the Landfeste.
1535	July 25: Due to the plague raging in Wittenberg, the University of Wittenberg moves to Jena for three quarters of a year and takes up residence in the empty former Dominican monastery.
1536	January 26: Three Anabaptists from the Orlamünde area are executed at the fortress. May: Barrels of illegally brewed beer are smashed in the village of Löbstedt to secure the town's privileges in brewing and serving beer ("beer wars").
1540	Elector Johann Friedrich issues a new city ordinance which, in addition to general provisions on city governance, contains numerous ordinances of a civil, police and criminal nature.
1542	According to the Turkish tax register, Jena has around 4,300 inhabitants.
1546	December 17: In the Schmalkaldic War, Jena pays homage to the Albertine Duke Moritz, one of Elector Johann Friedrich's opponents , for fear of attack .
1547	May 19: As a result of his defeat in the Schmalkaldic War, Johann Friedrich loseshis electoral dignity and around two thirds of his territory, including the university town of Wittenberg, in the "Wittenberg Capitulation". June 24: On his way to imperial captivity, John Frederick meets his eldest son near Jena to discuss the next steps to secure Ernestine rule. This includes the founding of a new university for the lost city of Wittenberg. July 10: Philipp Melanchthon is commissioned by the Ernestine rulers to write an expert opinion on the founding of a new state university. He advocates Jena as the location.
around 1548	The Burgkeller, a representative building in the Renaissance style at the eastern end of Johannisstraße directly next to St. Michael's Church, is completed. Sometimes referred to as the "Ratskeller", after 1815 the inn becomes a favorite banqueting house for the fraternity(ies) and is destroyed in 1945.
1548	March 19: In Jena, an "academic grammar school" is opened in the building complex of the former Dominican monastery as a preliminary stage of a new university. The first rector is the rhetorician and poet Johann Stigel. Alongside him, the theologian and philosopher Victorin Strigel, like Stigel a student of Melanchthon, teaches at the new educational institution. June 19: The first statutes are issued for the Akademisches Gymnasium in Jena.
1549	September: After temporary storage in Weimar, the majority of the Ernestines' private library is transferred to Jenaunder the direction of librarian Anton Heuglin and forms the foundation stone of the university library as the "Bibliotheca electoralis". One of its most valuable titles is the "Jenaer Liederhandschrift", a collection of Middle High German hymns written in the first third of the 14th century in northern central or northern Germany.
1552	September 24: The former Elector Johann Friedrich, released from imperial captivity , pays homage in Jena. Ernestine historiography soon moves the location of Johann Friedrich's meeting with the representatives of Jena's citizenry to the source of the Pennickenbach ("Fürstenbrunnen"), thus creating a place of remembrance in the history of the dynasty and the Reformation for centuries to come.
1553	November 30: After the Ernestines decide to have the reformer's works printed in Jena under the direction of Luther's confidant Georg Rörer in competition with the Wittenberg edition, a printing press is set up in the former Carmelite monastery and Christian Rödinger is granted the printing privilege.
1554	July 22: The foundation stone is laid for a municipal slaughterhouse of the Jena butchers' guild on Löbdergraben. August 16: A privilege is granted by the sovereign to operate the town pharmacy. Autumn: The appointment of Basilius Monner (law) and Johann Schröter (medicine) lays the foundation stone for a law and a medical faculty at Jena's high school.
1555	The first volume of the Jena Luther edition is published; by 1558, eight German and four Latin volumes are available.
1556	August 27: Construction of the tower of St. Michael's Church is largely completed with the addition of the spire cap.
1557	The printer of the Jena Luther edition, Christian Rödinger, publishesJohann Walter's"Magnifikat octo tonorum" , the first printed music in Jena. Until the end of the 17th century, the city is one of the main centers of music printing in the German-speaking world. April 27: The appointment of Matthias Flacius Illyricus, notorious for his rude attacks on his opponents , as Professor of Theology at Jena's High School cements its reputation as a place of "strict (pure) Lutheranism". August 15 (31): Emperor Ferdinand I signs the privileges for the University of Jena.
1558	February 2: The University of Jena is opened with a ceremonial act in the presence of the Ernestine dukes. The first rector is the physician Johann Schröter. Schröter sets up a second pharmacy in his house in Löbdergasse ("Schroetersburg").
1561	The university acquires the "Rosenhain Estate" in Johannisgasse. The "Rosen complex" is built between Johannisgasse and Fürstengraben as a second university site alongside the former Dominican monastery, which is rededicated as the "Collegium Jenense". Philipp von Herden, one of the wealthiest citizens of Jena, is documented as the landlord of the "Zur Sonne" inn on the market square. December 10: The impeachment of Matthias Flacius and his followers and their subsequent expulsion from the country marks the end of fierce theological disputes at the university. These had reached their climax in 1559/60 with the temporary imprisonment of Victorin Strigel, Flacius' main opponent .
1564	The chapel of the Nikolai Hospital is set up as a student hospital (demolished in 1784). April 14: The city and the university reach a settlement over the projectile. Only the professors' houses that they themselves occupy are tax-free. Overall, most of the privileges of the academic citizens remain untouched.
1565	A music-making community of citizens and students, the "Societas musicalis", known from 1595 as the "Collegium musicum", is founded.
1566	September 1: The Court of Justice, the supreme court of the Ernestines, moves into its new seat in Jena and meets here for the first time. The "Jenaer Schöppenstuhl" also exists as a legal expert committee, which is recruited from members of the university's Faculty of Law. The privilege of providing expert opinions for its Faculty of Law was granted to the university in the imperial foundation charter of 1558.
1569	March 7: The Ernestine consistory as the state's spiritual authority is relocated to Jena and is based here until 1612.
1570	May 21: A sovereign privilege is granted to the university pub "Zur Rosen" for the tax-free serving of wine and beer ("Rosenprivileg") to university members.
1571	The bronze tombstone for Martin Luther, probably cast in 1548/49 according to a design by Lukas Cranach the Elder, is placed in St. Michael's Church. The first city view of Jena, a copperplate engraving by Johann Mellinger (rector of the Latin school in Jena since 1569), is published.
1586	A botanical garden is established in the Collegium Jenense for the instruction of medical students (the second oldest scientific botanical garden in Germany).
1587	Autumn: With the appointment of Wolfgang Heider as Professor of Dialectics and Ethics (later Morals and Politics), philosophy develops into an independent academic discipline at the University of Jena.
1590	August 27: A guild regulation for bakers is handed down, which replaces regulations from the beginning of the 15th and 16th centuries that have not survived. It lists 23 bakeries in Jena.
1594	The church of the Dominican monastery, devastated in 1525, is restored as a collegiate church (university church). The sculptor and master builder Nikolaus Theiner (the Elder)from Lobeda designs the Renaissance tomb for Andreas and Katharina Schrot in St. John's Cemetery.
1596	The "Haus im Sack" is built as a tanner's residence and craftsman's house in Oberlauengasse.