This church is the former seminary church of the Würzburg Jesuit College and now the Catholic Church of St Michael. There has been a church on this site since the earliest 13th century. The first was a small chapel dedicated to St Agnes and used as a monastery by the Franciscans. During the 16th century the monastery was dissolved and the building complex was used as a training centre by the Jesuits. Between 1606 – 1610, the Jesuits built their first church dedicated to St Michael and St Agnes.

The current church was built during the years 1765 – 1798 to the designs of Johann Philipp Geigel and Johann Michael Fischer. However, in 1773 the Jesuit Order was abolished by Pope Clement XIV so the newly built church was used as seminary church after it was consecrated. Later it became the central confirmation church for the Würzburg city area.

During a bombing raid on 16th March, 1945 the church was destroyed with only the the outer walls and vaults holding up. The church was restored over the following 10 years in a modest and functional style and the new altar was consecrated in 1955. With the 400th anniversary of the Würzburg Seminary in 1989, the diocese commissioned a full artistic redesign of the church by Heinrich Gerhard Bücker. The theme of this redesign was the Revelation of St John the Divine.