After the transaction of sovereignty to the Imperial Abbey, the Reformed inhabitants of Toggenburg were promised by their Swiss allies of the Cantons of Zürich and Bern and by the prince-abbot that the principle of equal treatment in religious matters would be respected.

In the 17th century the prince-abbots and their worldly magistrates, the Landeshofmeister, began to organise the abbatial sovereign territories more strictly and to subject them to an at least tentatively modern governance in the frame of the absolutist practice of the day.

In 1663, for example, the abbatial governor of Toggenburg in Lichtensteig, Wolfgang Friedrich Schorno, sentenced a vicar, Jeremias Braun, to death because he had allegedly committed blasphemy during a Reformed sermon.

In 1695, in the framework of the Counter-Reformation, the seven Catholic cantons of the Confederacy and the prince-abbot of St Gall formed an alliance for the salvation of Catholicism against the "un-Catholic religion".

To strengthen the connections between the Imperial Abbey and Catholic Central Switzerland, Schwyz proposed to Prince-Abbot Leodegar Bürgisser (r. 1696–1717) in 1699 the construction of a new road over the Ricken Pass between Uznach and Wattwil.

After the settlement of the "Cross War" with the Reformed Imperial City of St. Gallen in 1697, Bürgisser ordered the municipality of Wattwil to start constructing the road over the Ricken Pass on the Toggenburg side through socage.

The refusal of the Wattwilers to collaborate in building the road, which they regarded as a threat to their religious freedom and as leading to their financial suppression, caused a serious conflict with the prince-abbot, who eventually resorted to incarcerating the highest Toggenburg magistrate, the Landweibel Josef Germann, in order to break the opposition.

In that situation, Landeshofmeister Fidel von Thurn moved Bürgisser to seek diplomatic ties within the Holy Roman Empire, and a treaty of protection was concluded with Emperor Leopold I of Habsburg in 1702.

Attempts at mediation by both Imperial and French envoys to the Confederacy failed, and the Reformed cantons urged for settling the conflict before the end of the War of the Spanish Succession to reduce the chance of a foreign intervention.

The struggle reached such a peak that the Toggenburgers armed themselves with the support of Zürich, and they occupied the abbatial fortresses at Lütisburg, Iberg and Schwarzenbach in 1710.

The "Pines" then militarily occupied the municipalities, the abbatial goods and the monasteries of Magdenau and Neu St. Johann with the tacit approval of Bern and Zürich.

Bern and Zürich found support with the city of Geneva and the Principality of Neuchâtel as well as its allies in the Prince-Bishopric of Basel: Biel, Moutier and La Neuveville.

Bern opened the first war phase on 26 April, when its first troops crossed the river Aar at Stilli to support Zürich with the occupation of Thurgau and the assault on the abbatial lands.

The five cantons occupied the cities of Baden, Mellingen and Bremgarten with their strategic fords and thereby threatened to drive a wedge between Zürich and Bern.

The second and much bloodier phase of the war was triggered by the Landsgemeinden of Schwyz, Zug and Unterwalden who, after being influenced by the papal nuncio, Giacomo Caracciolo, had rejected the Treaty of Aarau.

[8] After their victory in the Second Battle of Villmergen, the Bernese and the Zürichers advanced into the Lucernese territory, the land of Zug, across the Brünig Pass to Unterwalden and via Rapperswil to the Linthebene.

[9] At the Peace of Aarau [fr] of 11 August 1712, the Fourth Landfrieden in the history of the Confederacy, Bern and Zürich secured their rule over the Gemeine Herrschaften.

In the Landvogteien Thurgau, Baden, Sargans and Rheintal, the Reformed municipalities kept the guarantee of their religious exercise under Zürcher sovereignty, and the rights of the Catholics were secured.

Because of what he considered to be outrageous damage to the rights of the Imperial Abbey, as well as the danger posed to the Catholic religion in Toggenburg, Bürgisser obtained the Peace of Rohrschach, which was finally approved on 28 March 1714 after a series of negotiations with Zürich and Bern.

The animosity between the Imperial Abbey and Toggenburg increased further until the abolishment of the monastic state in 1798, after two abbatial magistrates had been murdered in 1735 and after a 1739 conference in Frauenfeld between the parties had failed to yield any results.