When he took control of the Bohemian lands in the 1520s, their religious situation was complex.
Its German population was composed of Catholics and Lutherans.
Some Czechs were receptive to Lutheranism, but most of them adhered to Utraquist Hussitism, while a minority of them adhered to Roman Catholicism.
A significant number of Utraquists favoured an alliance with the Protestants.
At first, Ferdinand accepted this situation and he gave considerable freedom to the Bohemian estates.
In the 1540s, the situation changed.
In Germany, while most Protestant princes had hitherto favored negotiation with the Emperor and while many had supported him in his wars, they became increasingly confrontational during this decade.
Some of them even went to war against the Empire, and many Bohemian (German or Czech) Protestants or Utraquists sympathized with them.

Ferdinand and his son Maximilian participated in the victorious campaign of Charles V against the German Protestants in 1547.
The same year, he also defeated a Protestant revolt in Bohemia, where the estates and a large part of the nobility had denied him support in the German campaign.
This allowed him to increase his power in this realm.
He centralized his administration, revoked many urban privileges and confiscated properties.
Ferdinand also sought to strengthen the position of the Catholic church in the Bohemian lands, and favoured the installation of the Jesuits there.
When he took control of the Bohemian lands in the 1520s, their religious situation was complex. Its German population was composed of Catholics and Lutherans. Some Czechs were receptive to Lutheranism, but most of them adhered to Utraquist Hussitism, while a minority of them adhered to Roman Catholicism. A significant number of Utraquists favoured an alliance with the Protestants. At first, Ferdinand accepted this situation and he gave considerable freedom to the Bohemian estates. In the 1540s, the situation changed. In Germany, while most Protestant princes had hitherto favored negotiation with the Emperor and while many had supported him in his wars, they became increasingly confrontational during this decade. Some of them even went to war against the Empire, and many Bohemian (German or Czech) Protestants or Utraquists sympathized with them.
Ferdinand and his son Maximilian participated in the victorious campaign of Charles V against the German Protestants in 1547. The same year, he also defeated a Protestant revolt in Bohemia, where the estates and a large part of the nobility had denied him support in the German campaign. This allowed him to increase his power in this realm. He centralized his administration, revoked many urban privileges and confiscated properties. Ferdinand also sought to strengthen the position of the Catholic church in the Bohemian lands, and favoured the installation of the Jesuits there.
Ferdinand I, Holy Roman Emperor