The Protestant Reformation sparked numerous wars of religion, which culminated in the 30 Years War.
The German lands were referred to as "The Holy Roman Empire" in those days. Immediately following the death of Martin Luther, the prominent German leader of the Protestants, war broke out between the forces of the Holy Roman Emperor, Charles V, and Lutheran princes. Charles V went to war against the Lutheran princes in the Smalcald Wars (1546-57) to try to force them back into adherence to Catholicism. There were ongoing struggles in the years after that, and ultimately, the Thirty Years War (1618-1648) was waged in the German territories (aka the Holy Roman Empire) over religious and other issues.
There were continuing issues of conflict in German territories between Lutherans and Catholics, which were even exploited after the unification of Germany. Chancellor Otto von Bismarck led a Kulturkampf ("culture war") against the Roman Catholic Church's influence in Germany.