Nieuwenaar encouraged the Prince-elector and Archbishop of Cologne Gebhard Truchsess von Waldburg to retain his control of the Electorate of Cologne after he married Agnes von Mansfeld-Eisleben and converted to Calvinism. In 1583 Pope Gregory XIII excommunicated Gebhard, and the Cathedral chapter chose Ernest of Bavaria as the new Elector. War broke out between the two rivals: it was known as the Cologne War. Gebhart was supported by Nieuwenaar (as his general), his brother, Karl, Truchsess von Waldburg-Trauchburg and the Dutch rebels. Ernest by his brothers, Wilhelm V, Duke of Bavaria, Ferdinand of Bavaria, and eventually by Spain. By 1586, Nieuwenaar was driven out of all his German possessions.