As a consequence of the 1801 Treaty of Lunéville, Würzburg, along with the other ecclesiastical states of Germany, was secularized in 1803 and absorbed into the Electorate of Bavaria.

In the 1805 Peace of Pressburg, Ferdinand lost Salzburg to the Austrian Empire, but was compensated with the new Grand Duchy of Würzburg, Bavaria having relinquished the territory in return for the Tyrol.

The name "Franconia" fell out of usage, but the bishop revived it in his own favour in 1442 and held it until the reforms of Napoleon Bonaparte abolished it.

The charge of the original coat of arms showed the "Rennfähnlein" banner, quarterly argent and gules, on a lance or, in bend, on a blue shield.

The Rechen and the Rennfähnlein represented the diocese, while the other (usually two) fields showed the personal coat of arms of the bishop's family.