The Thirty Years' War (1618–1648) began in Bohemia with the Bohemian Revolt, a reaction against the Catholic Habsburgs' increasing suppression of Protestant freedoms in the Holy Roman Empire. Tensions erupted after Emperor Matthias designated his Catholic cousin, Ferdinand II, as his successor, despite Ferdinand’s staunch anti-Protestant stance. Protestants feared he would revoke the freedoms promised in the Letter of Majesty, leading to the 1618 Defenestration of Prague, where Protestant nobles threw two of Ferdinand's Catholic officials from a castle window. This incident symbolized open resistance against Habsburg authority and triggered a European conflict centered on religious and political tensions within the Holy Roman Empire.
Protestant estates in Bohemia raised an army and declared Frederick V of the Palatinate, a Protestant, as their king, challenging Habsburg control. In response, Ferdinand II, Matthias’s successor, allied with the Catholic League and gathered forces to quell the rebellion. The decisive Battle of White Mountain in 1620 saw the Bohemian forces defeated near Prague, leading to harsh reprisals. Protestant nobles faced executions, while widespread land confiscations placed Bohemian properties in the hands of Catholic nobles, many of whom were loyal German allies. This decisive loss began an era of forced re-Catholicization, where the Habsburgs expelled Protestant clergy, confiscated noble lands, and imposed Catholic practices. The confiscated estates were distributed to loyal Catholic nobility, many from Germany, leading to significant Germanization in the Czech lands.
As the war expanded across Europe, Bohemia, Moravia, and Silesia became key battlegrounds, enduring relentless invasions and occupations by various foreign armies, drawing in Denmark, Sweden, and France, each with its own interests in limiting Habsburg power. Bohemia and Moravia, central battlegrounds during the war, suffered extensive devastation from occupation, looting, and disease. Notable Czech-born military leaders included Albrecht von Wallenstein, who initially fought for the Habsburg side before aligning with Protestant interests, and Jan Amos Comenius, a Protestant theologian who went into exile, symbolizing the cultural loss in Bohemia.
Local economies and communities were devastated, with villages, castles, and cities looted or destroyed. The war's devastation was so severe that, by its end in 1648, Bohemia had lost nearly two-thirds of its population, with some areas seeing up to a 50% decline due to famine, disease, and heavy military losses.
In 1648, the Treaty of Westphalia formally ended the conflict, confirming Habsburg control and Bohemia’s subordination within the Empire. The treaty solidified Bohemia’s integration into the Habsburg monarchy and centralized rule from Vienna. This period, often referred to as the "Dark Age" in Czech history, resulted in the suppression of Czech Protestant culture, forced Catholic conformity, and widespread Germanization that would shape the Czech lands for centuries.