Despite the initial successes of the Reformation in the strongest and most populous parts of the Confederation, the Catholics mobilised their forces to strike back.

Secular authorities in the Catholic areas took over many of the roles of the bishops in such matters as justice and finance, and in some cases even the appointment of priests.

Following the upsurge in learning promoted by the Reformists, many of the Catholic areas too started a programme of education, run by the Jesuits.

A great contribution to the Catholic renewal in Switzerland was made by Cardinal Carlo Borromeo (1538-1584). Among other things, he set up the Collegium Helveticum in Milan in 1579 to train Swiss clergy. Borromeo was canonised in 1610 and is regarded as the patron saint of Catholic Switzerland (and also of Monterey in California.)

The Catholics also won back some territory on the ground. Some of the common lordships readopted Catholicism after the defeat of Zurich in 1531. In 1567 Bern gave the Chablais and Pays de Gex back to Savoy and they returned to Catholicism, as did some of the territories recovered by the Bishop of Basel in 1581. Valais also slowly gave up the reformed religion after the intervention of the Catholic cantons.¨

However, other regions remained steadfastly reformist despite pressure. They included the Toggenburg, although it belonged to the St Gallen monastery. In cantons where each parish was able to choose its own faith, Glarus stayed biconfessional and Appenzell split in 1597 into Catholic Inner Rhodes and Protestant Outer Rhodes.