Augmented by the Berchtesgaden Provostry and parts of the former prince-bishoprics of Eichstätt and Passau, his lands were reorganized as the Electorate of Salzburg, created for Archduke Ferdinand of Habsburg-Lorraine, younger brother of Emperor Francis II.

He established the Faculty of Medicine at the Salzburg University and installed the distinguished pedagogue Franz Michael Vierthaler to introduce an education reform.

He also ordered the improvement of mountain pass roads to Bad Gastein, Sankt Johann im Pongau and Radstadt, while his economic reforms roused opposition by the Salzburg guilds.

When in October 1805 French troops again moved in during the War of the Third Coalition, Ferdinand, like his predecessor Archbishop Colloredo, had to leave his residence for his brother's court in Vienna.

After the War of the Fifth Coalition it passed to Bavaria according to the 1809 Treaty of Schönbrunn, incorporated into the Salzach District together with Tyrolean Kitzbühel, Traunstein and Ried im Innkreis in 1810.