[1] Around 1183, a church was built on the present site, donated by the patricians Walter Kerlinger and Dietrich Hotermann as well as Conrad Brun and Heinrich de Stalberg.

[2] Then, between 1278 and 1290 – under the long-time pastor Heinrich Bauso – a choirless Gothic hall was built, the core of today's church.

[2] Around 1500, the Trinity Chapel was completed, donated by the pastor, theology professor, multiple dean and rector of the university, Auxiliary Bishop Johannes Bonemilch von Lasphe.

Martin Luther, who studied in Erfurt between 1501 and 1505, regularly attended masses in St Michael's Church.

Luther's friend Johannes Lang, the reformer of Erfurt, preached in St Michael's Church from 1530 and was buried here in 1548.

Since Pentecost 2007, it has also served as a place of worship for the "Old Catholic Community of West Thuringia / Erfurt", which holds services there on every second and fourth Sunday of the month.

Finally, it was decided to have Ludwig Compenius build a new instrument from the material of the old organ and that of the demolished St George's Church.

[6] In 1896, the Wilhelm Rühlmann company from Merseburg built a new pneumatic instrument for which only parts of the old organ were reused.