The Habsburgs were pious Catholics and tried to contain and eventually defeat Protestantism. Multiple examples can be given:

1. Charles V and the Treaty of Augsburg (1555) In which Holy Roman Emperor Charles V gives the princes in the HRE the freedom to decide the religion in their territory. But the people had to follow the religion of the prince. This was called 'cuius regio, eius religio', translated 'whose territory, his religion'. This treaty was the official acknowlegdement of the religious division of the HRE.

2. Philip II and the Dutch Revolt During the early 16th century most Dutch provinces (in personal union under the Habsburg crown) converted to Calvinism. Philip II tried to stop this spread by setting up the Inquisition and burning heretic noblemen. These religious tensions, together with economic and political factors, lead to the outbreak of the Dutch Revolt in 1568. According to J.C.H. Blom the Dutch weren't used to this hard crackdown and in the Union of Utrecht (1597) they declared a defensive league and, among other freedoms, freedom of conscience. This lead to an exceptional tolerance of religious difference in the later Dutch Republic.

3. Habsburg Austria and the Thirty Years' War In 1618 multiple factors, such as the rise of Calvinism in Germany, power struggles between Spain, France, Nordic states and German states led to the outbreak of the Thirty Years' War. The main casus belli is, according to most historians, the Bohemian Revolt of 1618-1621, in which Bohemia switched to Calvinism. In a few years the HRE, and most Europeans powers were divided in two leagues, Pro- and Anti-Habsburg alliances. The Thirty Years' War evolved from a religious struggle to a major proxy and active war for most European powers. In 1648 all powers signed the Treaty of Westphalia, ending the Thirty Years' War, and concurrently aswell the Dutch Revolt.

Sources: J.C.H. Blom, History of the Netherlands J. Merriman, History of Modern Europe, part I