The Obermünster ("higher monastery", named in relation to the older Niedermünster, or "lower monastery"), dedicated to the Assumption of the Virgin Mary, was founded in the early 9th century by the ruling house of the Carolingians as a Benedictine nunnery to complement the adjacent St. Emmeram's Abbey.

It passed almost immediately into the possession of the bishops of Regensburg, at that date also abbots of St. Emmeram's, but King Louis the German recovered it by exchanging Mondsee Abbey for it in 833.

The nunnery and its church were destroyed by fire in 1002, and was rebuilt and revitalised by Emperor Henry II, who is traditionally considered its founder, and who made it an Imperial abbey — judicially independent, but in this case without territorial sovereignty.

[citation needed] In 1219 it was put under Papal protection and in 1315 Emperor Louis the Bavarian elevated the abbesses to the Reichsfürstentum, or Imperial principality, after which they were known as Princess-abbesses ("Fürstäbtissinnen").

Repeated attempts to reform the rule of life and to return the house to its original Benedictine practice failed and in 1484 Obermünster formally became a collegiate house for noblewomen (adlige Frauenstift), which is what it had in any case been in practice for many years.