section_path: Wars of religion and tolerance/Counter-Reformation and regional conflicts
section_name: Counter-Reformation and regional conflicts
paragraph_text: Counter-Reformation and regional conflicts
  
  The continuous expansion of Protestantism stopped in Germany after the Peace of Augsburg. The Bavarian duke Albert V (r. 1550–1579) took the lead of recatholicisation. He overcame the opposition of Evangelical nobles, and exiled all clerics who refused to take the Tridentine oath. With Albert's support, the Jesuits opened a college in Ingolstadt that accepted Evangelical and Hussite students. Emperor Ferdinand I's eldest son and successor, Maximilian II (r. 1564–1576) pursued a tolerant religious policy but his brothers, Ferdinand II of the Tyrol (r. 1564–1595) and Charles II of Inner Austria (r. 1564–1590) were determined to subdue their Protestant subjects. After the predominantly Evangelical Estates of Inner Austria who controlled taxation extracted concessions from Charles II, he promoted Catholicism by appointing Catholics to state offices even if he needed to hire Bavarian and Tyrolian nobles.
  
  Interreligious conflicts led to wars in many regions of Central Europe. The Cologne War broke out after Gebhard Truchsess von Waldburg, Archbishop-elector of Cologne (r. 1577–1583), abandoned Catholicism and married his Protestant lover Agnes von Mansfeld-Eisleben (d. 1637) in 1582. The war ended with the victory of his Catholic opponent Ernest (r. 1583–1612), a younger son of Albert V. The Strasbourg Bishops' War began when both the Catholic and Protestant canons of the Strasbourg Cathedral elected their own candidate to the see of Strasbourg in 1592. At the end, the Protestant candidate Johann Georg von Brandenburg (d. 1624) renounced in favor of his opponent Charles of Lorraine (r. 1592–1607).
  
  Charles II's son and successor Ferdinand II (r. 1590–1637) set up "reformation commissions"—a group of clerics and state officials led by a senior clergyman—to visit the Inner Austrian parishes between 1598 and 1601. The commissioners seized and destroyed Evangelical churches, burned Protestant books and expelled Evangelical priests, often with the support of the local (mainly Slovenian) peasantry. His cousin Emperor Rudolf II (r. 1576–1612) introduced anti-Protestant measures in Royal Hungary and Transylvania, provoking a rebellion. The Ottomans supported the rebels whose leader, the Reformed aristocrat Stephen Bocskai was proclaimed prince of Transylvania (r. 1605–1606). Rudolph appointed his brother Matthias to conduct negotiations with Bocskai, and the peace treaty sanctioned the freedom of the Evangelical and Reformed Churches in Royal Hungary in 1606. Rudolph was forced to cede Hungary, Austria and Moravia to Matthias in 1608, and to confirm religious freedom in Bohemia in 1609.