Whilst situated within the Ortenauer Reichslandvogtei, under the protection of Rudolph of Habsburg (1273–91), the territory's protectors were an array of local lords: the Zähringen were followed in 1218 by the Staufen dukes of Swabia and in 1245 by the bishops of Strasbourg until the 1550s.

These Vögte and confirmations of their rights — both Papal (1139, 1235, 1252, 1287) and Imperial (1309, 1331, 1516) — ensured the Abbey's continual independence.

Gengenbach was deeply embroiled in the Investiture Controversy and two of its abbots were driven out for supporting the Imperial rather than the Papal cause.

A pipe organ with an historical eighteenth century the casing from the former abbey church is now in the Augustiner Museum in Freiburg im Breisgau.

The abbey was mediatized in the wake of the German Mediatisation of 1803, and shortly afterwards its territories were absorbed into the state of Baden.