The first historical mention appears in 1073 when Welf I gifts the by then already built Augustinian monastery large lands on both sides of the Ammer river.

Emperor Luois the Bavarian in the 14 century was patron of the abbey, and this as well as its being on the pilgrimage route to Italy, made Rottenbuch become the most influential house of Canons Regular (community of priests) in Germany.

The medieval interior of the church was redecorated in the 18th century to the very ornate High Baroque style by the painter Matthäus Günther and stuccoist Josef Schmuzer.

In 1803, under the Reichsdeputationshauptschluss 1803 (which "secularized nearly 70 ecclesiastical states and abolished 45 imperial cities"), the monastic buildings were pulled down and the noteworthy contents of the library were sent to a paper mill.

The village was part of the electorate of Bavaria and formed a closed "Hofmark" (a type of partnership) together with Böbing, Wildsteig, and Schönberg.