Following a huge fire in the period between the original foundation and the reconfirmation in 1237, several nobles of the surrounding area provided means for reconstructing the monastic buildings.

In the Later Middle Ages Gutenzell Abbey gradually managed to achieve imperial immediacy, the legal basis of which was formed by two privileges by Emperor Sigismund in 1417 and 1437.

In 1525 the abbey was looted by revolting farmers of the Baltringer Haufen during the German Peasants' War.

During the Thirty Years' War the nuns fled approaching Swedish troops to Styria in 1632.

In the second half of the 18th century the last major refurbishment of the monastery church was carried out in 1755-56 by the Wessobrunn stuccoist Franz Xaver Feuchtmayer the Elder, possibly following plans by Dominikus Zimmermann, whose daughter Maria Alexandra was prioress at the time.

The pulpit from 1756 was made by Stephan Luidl who also created the high altar in 1762, possibly also to designs by Dominikus Zimmermann.

In 1803, the abbey was dissolved during secularisation and its assets transferred first to the Counts of Toerring, and then in 1806 to the Kingdom of Württemberg.