Wettingen-Mehrerau Abbey is directly subordinate to the Holy See and thus forms no part of the Catholic Archdiocese of Salzburg.

Little information survives on the history of either foundation up to 1079, when the monastery was reformed by the monk Gottfried, sent by abbot William of Hirsau, and the Rule of St. Benedict was introduced.

In particular Ulrich Mötz, later abbot, exerted much influence in the Bregenz Forest by his preaching against the spread of religious innovations while he was provost of Lingenau (1515–33).

However, the Treaty of Pressburg (1805) gave Vorarlberg, and with it the abbey, to Bavaria, which under the "Reichsdeputationshauptschluss" had already secularised its own religious houses in 1802–03.

When the district came again under the rule of Austria, the surviving monastic buildings were used for various purposes until in 1853 they were bought, with the permission of Emperor Franz Joseph I, from the last owner, along with some pieces of land connected with them, by the abbot of the Cistercian Wettingen Abbey in Switzerland, a monastery which had been forcibly suppressed by the Canton of Aargau in 1841, and for thirteen years had been seeking a new home.

The monastic buildings were extended, and in 1859 a new Romanesque church was built; of particular note is the monument to Cardinal Hergenröther (died 1890), who is buried there.

In 1919 Wettingen-Mehrerau bought the pilgrimage church at Birnau and the nearby Schloss Maurach, which to this day it runs as a priory.