Given its isolation through marshy terrain and hills, it was only first documented in 1222 when the Abbot of Salem purchased the tithes of the village from the Lords of Vaz.

The conflict of rights between the abbot and the prince-bishop led to a series of disputes that were mediated by town jurors; the first of which occurred in 1295.

Plague, crop failures, and a decrease in the price of grain devastated the community in the 14th century, and slowly the prince-bishopric lost influence in the region.

In the Reichsdeputationshauptschluss of 1803, in which the principalities of the ecclesiastic rulers were dispersed to the counts and princes of the empire, Daisendorf was given to the Electorate of Baden.

The village has an ancient chapel St. Martin, which was built in 1508 and holds unique fresques of the renaissance age.