At the time of its dissolution in 1802, the Imperial Abbey covered 112 square kilometers and had about 5,000 subjects.

Abbot Jakob Köplin (1548–1600) succeeded in having St. Ulrich and Afra's long standing claim to Imperial immediacy (German: Reichsfreiheit) recognized in 1577, thus confirming the abbey as a self-ruling Imperial estate, but this status was bitterly contested by the bishops of Augsburg, and the legal conflict was resolved in favour of the abbey only in 1643/44.

Inside Augsburg however, St. Ulrich and Afra's sovereign rule extended only over the grounds of the abbey church and monastery.

In 1805 a French military hospital was installed here; after six monks, including the abbot, had died of infectious diseases, the remainder moved into a private house.

On the site the "Haus St. Ulrich" has stood since 1975, an academy and pastoral centre of the Diocese of Augsburg.