The church was built by William V, Duke of Bavaria between 1583 and 1597 as a spiritual center for the Counter Reformation. The foundation stone was laid in 1585.
In order to realise his ambitious plans for the church and the adjoining college, Duke Wilhelm had 87 houses in the best location pulled down, ignoring the protests of the citizens. The church was erected in two stages. In the first stage (1583-88), the church was built by the model of Il Gesù in Rome and given a barrel-vaulted roof by an unknown architect, the vault being the largest in the world apart from that of St Peter's in Rome, spanning freely more than 20 meters. When the church was built, there were doubts about the stability of the vaulting. But it was the tower that collapsed in 1590, destroying the just completed quire. Duke William V took it as a bad omen and so planned to build a much larger church. The second phase of construction continued until the consecration of the church in 1597. Friedrich Sustris built on to the undamaged nave a new quire and a transept and a magnificent facade.
The facade is impressive and contains standing statues of Duke Wilhelm and earlier rulers of the Bavarian Wittelsbach dynasty, cast in bronze, in the form of a family tree. Hubert Gerhard's large bronze statue between the two entrances shows the Archangel Michael fighting for the Faith and killing the Evil in the shape of a humanoid demon.
Having suffered severe damage during the Second World War, the church was restored in 1946-48. Finally, between 1980 and 1983, the stucco-work was restored.
The church crypt contains the tomb of Eugène de Beauharnais. A monument was erected by Bertel Thorwaldsen in 1830 in the church. Eugène was the son of Josephine de Beauharnais, Napoleon's wife and her first husband, general Alexandre de Beauharnais. He married a daughter of King Maximilian I of Bavaria in 1806 and was created Duke of Leuchtenberg in 1817. In the right transept, there is a cross monument of Giovanni da Bologna.
The crypt contains among others the tombs of these members of the Wittelsbach dynasty:
- William V, Duke of Bavaria
- Maximilian I, Elector of Bavaria
- King Ludwig II of Bavaria
- King Otto of Bavaria