The last time Europe went to war over religion was the 30 Years War, that ended in 1648. And by the last years it had little to do with religion and everything to do with who would be dominant in Germany: Austria, France or Sweden.
There were at least eight general European wars after (depending on how you count the French Revolutionary Wars and Napoleonic Wars, as one or many), and none were over religion.
Religious Wars were fought throughout the 20th century in Europe: mainly against Christians butchered by the millions at the hands of Nazis, Muslims, and Communists.
Jews suffered disproportionately, although not exclusively, at the handss of the Pagan German Nazis.