It is also possible that the seat of the diocese of Augusta Raurica had intermittently been moved to Basel already in the 7th century, with one Ragnacharius mentioned as Augustanus et Basileae ecclesiarum praesul in the vita of Eustace of Luxeuil (d. 629).

After the death of Rudolph in 1032, the vassalage was converted to imperial immediacy, elevating the Bishop of Basel to the status of Prince-Bishop, ranking as an ecclesiastical prince of the Holy Roman Empire.

During the 15th century, however, a number of politically and militarily successful bishops managed to regain some of the previously lost territories and Basel began to align itself with the Old Swiss Confederacy as an "associated city" (Zugewandter Ort).

Prince-bishop Christoph von Utenheim held on as bishop of Basel for a few years, but the slow decline of his authority forced him to resign, on 19 February 1527.

The Prince-Bishopric lost the bulk of its remaining territories to the Rauracian Republic in 1792 (revolutionarily converted into the French département of Mont-Terrible in the following year), while the treaty of Campo Formio in 1797 gave international recognizance to the French annexation, which could be expanded to all the bishopric territory (while Switzerland received Austrian Fricktal as indemnity), which retained Schliengen as its sole dominion.

Schliengen was made part of the Margraviate of Baden in the resolution of the Reichsdeputationshauptschluss of 1803, discontinuing the status of the bishops of Basel as secular rulers.