During the Thirty Years' War, Switzerland was a relative "oasis of peace and prosperity" (Grimmelshausen) in war-torn Europe, mostly because all major powers in Europe were depending on Swiss mercenaries, and would not let Switzerland fall in the hands of one of their rivals. Politically, they all tried to take influence, by way of mercenary commanders such as Jörg Jenatsch or Johann Rudolf Wettstein . The Drei Bünde of Grisons, at that point not yet a member of the Confederacy, were involved in the war from 1620, which led to their loss of the Valtellina in 1623.

Political power congealed around the 13 cantons ( Bern, Zürich, Zug, Glarus, Uri, Schwyz, Unterwalden, Fribourg, Solothurn, Basel, Luzern, Schaffhausen, Appenzell) of the old confederation. During this area, the patrician families decreased in number but increased in power. Some patrician families were drawn from leadership in the Guilds or trading groups within the town. While other families grew from successful mercernary captains and soldiers. The trend toward increasing Authoritarianism conflicted with the history of public expression which grew out of the Swiss Reformation. In many regions the patrician families were unable to suppress the public assemblies but they did dominate the assemblies. The tradition of inviting the people to express their opinions died out mostly during this era.

At the Treaty of Westphalia in 1648, Switzerland attained legal independence from the Holy Roman Empire. The Valtellina became a dependency of the Drei Bünde again after the Treaty and remained so until the founding of the Cisalpine Republic by Napoleon Bonaparte in 1797.

In 1653, peasants of territories subject to Lucerne, Berne, Solothurn and Basel revolted because of currency devaluation (Bauernkrieg). The rebels laid siege to Lucerne and Berne, but a compromise was reached before the outbreak of violence. The social and confessional tensions remained, however, and erupted again in the Battles of Villmergen in 1656 and 1712.