- 1559 - The first Jesuits arrive in Munich, invited by Duke William V.
- 1590 - Anton Neuknecht erects a first organ in St. Michael's. The instrument originates from the St. Lorenz chapel in the Old Court. Melchior Lachmair is responsible for the new case.
- 1597 - The completion of St. Michael's Church prompts the construction of its first actually new organ. Urban Heusler builds the instrument.
- 1697 - For the first centenary celebration of the church, the organ is taken down and replaced with a new instrument by Johann Fux. The prospectus is designed by a Jesuit brother, Johann Hörmann, who also provided the design for the large baroque pulpit.
- 1812 - Dinkelsbühl organ builder Franz Joseph Reiner renews the organ's interior sets of pipes, wind system and trackers according to specifications by then famous organ virtuoso and theorist Abbé Vogler.
- 1896 - Munich organ builder Franz Borgias Maerz constructs a new organ according to tonal specifications by Joseph Gabriel Rheinberger. His work is funded by a generous testamentary bequest of 20,000 gold marks from Rheinberger's wife Franziska, who had died in 1892. Maerz reuses the case from 1697, but significantly altered its proportions to make room for the necessary extensions of the new instrument.
- 1944 - On 22 November, St. Michael's is hit heavily by demolition bombs. The Maerz organ of 1896 is destroyed completely.
- 1953 - A new loft system is installed, which does not correspond to the nave structure. A small organ positive with two manuals and pedal is temporarily placed at one side.
- 1966 - The Schuster organ building company from Munich builds a new organ on this loft. The new instrument has 3 manuals and pedal. The swell-box is placed above the first side niche of the nave.
- 1982/83 - In the course of final post-war restoration works on the church, the island for the free-standing people's altar island is moved further back. Stucco work is completed, the old loft construction is restored. Based on the 1697 prospectus design by Jesuit brother Johann Hörmann, Dillingen organ building company Hubert Sandtner installs a new organ.
- 2006 - First considerations for a thorough renovation and expansion of the organ begin. They are followed by extensive consultations with the responsible experts and with renowned organists of the European concert scene.
- 2011 - The organ is reorganised and expanded with a German swell-box by the Rieger organ-building company from Vorarlberg/Austria (inauguration on 30 October 2011). The 17-century prospectus by Jesuit brother Johann Hörmann is retained, and the better part of the pipe material from the predecessor organ (Sandtner 1982/83) is re-used. The new Rieger organ allows stylistically accurate interpretations of very wide range of organ music and provides an ideal foundation for sophisticated improvisations.
Dr. Frank Höndgen