On 18 and 27 April 1763 he was elected the Bishops of Freising and Regensburg, respectively, but he abandoned these dioceses for the Archbishopric-Electorate of Trier and the Prince-Bishop of Augsburg in February and August 1768, respectively, where he already functioned as coadjutor since 1764.

He allowed the Jesuits to remain in Trier after abolishing their order, protested the radical reforms of his cousin, the Emperor Joseph II of Austria, and banned several processions and holidays.

He and the archbishopric-electorate were greatly affected by the success of the French revolutionary forces, and at the Treaty of Lunéville in 1801, he lost all lands of the electorate west of the River Rhine, retaining only a few small territories pertaining to Trier itself.

In 1803 he lost those as well, along with the Prince-Bishopric of Augsburg and the Prince-Provostry of Ellwangen Abbey, which were secularized and annexed by the princes of Nassau-Weilburg, the Elector of Bavaria, and the Duke of Württemberg, respectively.

Clemens Wenceslaus received a pension of 100,000 guldens and retired to Augsburg, dying in the episcopal summer residence in Marktoberdorf in Allgäu in 1812.