On 30 June 1602 in Sigmaringen, Johann married the three years younger Countess Johanna (1581–1634), the daughter of Count Eitel Friedrich IV of Hohenzollern-Hechingen.

Unlike their relatives who ruled the Electorate of Brandenburg, the Sigmaringen branch of the House of Hohenzollern had remained Catholic.

However, Sigmaringen was located in the immediate vicinity of the Evangelical Duchy of Württemberg, and thus on a prominent position in the escalating confessional conflict.

His financial situation allowed Johann to make substantial donations to the churches and monasteries in his territory and to further expand his Sigmaringen Castle.

Johann fled to Braunau am Inn, together with Duke Maximilian, whom he served as secret councillor.