During the High and the Late Middle Ages Wiblingen Abbey was famous for its scholarship and learning as well as being a place of exemplary monastic discipline due its strict adherence to the rule of St. Benedict.

On the initiative of Abbot Johannes Schlegel the Holy-Cross-Relic was hidden in order to protect it from marauding Protestant Swedish troops.

However, following the withdrawal of the Swedish troops the relic could not be recovered, since there was no one alive who remembered its hiding place, the witnesses to its concealment all having succumbed to the plague.

Due to the efforts of Abbot Benedict Rauh, whose term in office lasted from 1635 to 1663 and who also functioned as military bishop to the Bavarian army, the abbey managed to survive the calamities of the war.

The increasing economic and political importance under abbots Ernest Fabri, Maurus Falkner and Modest I led to the abbey being granted the status of an autonomous territorial Estate (Mediatstand) of Further Austria in 1701.

The structures of the medieval abbey had been continuously enlarged and changed during the previous centuries with the originally church having been built in the style of Romanesque architecture.

Works began with the building of the courtyards whose design was influenced by the plans for Einsiedeln Abbey by architect Caspar Moosbruger.

Due to financial strains the building of the church had not even started at the time of the death of Abbot Meinrad Hamberger (1730–1762).

His successor, Modest II (1762–1768), either showed no interest in continuing the building works or was suffering from lack of revenue to complete them.

However, he could not further his design since he was pushed aside by the fresco painter Januarius Zick, who had been educated to become an architect by Jakob Emele at Schussenried Abbey.

In 1806, the abbey became property of the newly founded Kingdom of Württemberg whereupon the Bavarian troops left after they had auctioned off all the remaining furniture.

The rest of the North wing and the adjoining former commercial buildings are now part of the University of Ulm, housing the School for Medical Documentation.