The abbey was founded in 1138 by Ulrich II, Bishop of Constanz as a private episcopal monastery, with the intention that it should offer shelter and hospitality to pilgrims on their way from Constanz to Einsiedeln Abbey.
The hermit Gebino was appointed the first abbot. In only six years he had had built a bell tower, accommodation for both monks and nuns, and a guesthouse. At its high point in about 1210, Fischingen had about 150 monks and 120 nuns. The "Vogtei" (protective lordship) over the abbey belonged to the Counts of Toggenburg. Saint Idda of Toggenburg, who lived in a cell of the abbey in about 1200, is buried in a chapel off the abbey church.
During the Reformation, the abbey was dissolved for several years, when in 1526 the abbot and the four remaining monks converted to the Reformed beliefs. The abbey was reopened however on the initiative of the Roman Catholic townships of the Old Swiss Confederacy.
In the 17th and 18th centuries the premises were rebuilt in the Baroque and Rococo styles. Between 1685 and 1687 a new abbey church was constructed, and in 1705 a new chapel dedicated to Saint Idda. In the 18th century part of the monastic premises was rebuilt, but could not be completed because of the abbey's accumulated debts.
After the repeal in 1973 of the so-called "Article of exception" ("Ausnahmeartikel") in the Swiss constitution, which forbade the opening of new monasteries and the re-establishment of old ones, Fischingen was reopened as an independent priory in its former premises in 1977.