However, two years later, this short-lived principality was annexed by the newly established Austrian Empire according to the Peace of Pressburg and Ferdinand received the Grand Duchy of Würzburg in compensation.

After the end of the Napoleonic Wars and the 1816 Treaty of Munich, the Salzburg lands came back to Austria, with the exception of the share on the left bank of the Salzach river, the so-called Rupertiwinkel, which, like the former Prince-Provostry of Berchtesgaden, remained in Bavaria.

Some smaller areas in the Ziller and Defereggen valleys fell to Tyrol; the town of Friesach was ceded to Carinthia.

Caroline Augusta of Bavaria, widow of the late Emperor Francis I of Austria, chose the city of Salzburg as her residence.

With the fall of the Austro-Hungarian Monarchy in 1918, the duchy was succeeded by the state of Salzburg, part of first German Austria and then the First Austrian Republic.