In 1367, the League of God's House was formed by members of the cathedral chapter, the bishop's own ministerialis, the city of Chur, and a number of jurisdictions of the prince-bishopric.

The reason was that Bishop Peter Jelito, who mostly stayed abroad, was suspected by his own subjects of planning to sell the prince-bishopric to the House of Habsburg, with a loss of independence looming.

The Three Leagues, in fact a republic ruled by local aristocrats, remained part of the Holy Roman Empire until 1798, but has been allied to the Old Swiss Confederacy since 1497.

The struggles of Switzerland for liberty in the fourteenth and fifteenth centuries, and, later, the secret preaching of Zwingli and Calvin, did great harm to the diocese, especially as the Catholic clergy neglected the instruction of the people.

The Reformation was publicly proclaimed at Chur in 1524, and the two Catholic churches of St. Martin and St. Regula were given over to the Protestants, who retain possession of them to this day.

[3] Twenty years later St. Charles sent the Capuchins into the endangered region, but Bishop Peter II (de Rascher) refused to admit them.

The first Capuchin superior of the mission was St. Fidelis of Sigmaringen, who, on his way from Sewis to Grüsch, a little north of Chur, was slain (24 April 1622) by peasants whom the sermons of the Protestant preachers had wrought up to a fury.

These two missions, Rhætiæ and Mesauci, were made prefectures Apostolic under the care of Italian Capuchins and these prefects resided in the towns of Obervaz and Cama, both in the Canton of Graubünden.

The Capuchin Theodosius Florentini, vicar-general from 1860 till his death (15 February 1865), was a very distinguished missionary; in 1852 he erected the Hospital of the Cross at Chur; before this he had already laid the foundations of two female religious congregations, one for the instruction of children, the other for the care of the sick.

Three Benedictine abbeys — Einsiedeln, Engelberg, and Disentis — are within the diocese and, with the church of Saint Nicholas of Flüe at Sachseln, are places of pilgrimage.

In 1997 the Archdiocese of Vaduz was erected by Pope John Paul II in the apostolic constitution Ad satius consulendum.