Originally established as a parish, the history of St. Michael's dates back to 1282, when a priest was first mentioned. Until 1525, the church belonged to a Cistercian monastery. The convent was dissolved during the Reformation.

The Reformation was of decisive importance for Jena and the surrounding area. Martin Luther preached several times in the town church. He often debated with students, friends and critics in Jena (Hotel Schwarzer Bär) and the surrounding area.
Inside the late Gothic hall church with its impressive façade is a Gothic stone pulpit from which Luther preached, as well as the original tombstone of the reformer, which was made in 1549 by the Erfurt bell founder Heinrich Ziegler based on a picture by Lucas Cranach the Elder.