The universal domain over which he hoped to reign faced external and internal threats; its desired unity and order were attacked by infidels from within and by national rivalries and heresy from within. He had looked at the first and second threats; Now he has turned his attention to the third. Protestantism had spread rapidly in Germany. More than one religion, in the 1540s it was a full-fledged political movement with increasing military capability. The number of Protestant territories has recently increased in Brandenburg, palatinate, Alberta Saxony and the dioceses of Cologne, Münster, Osnabrück, Naumburg and Merseburg, among others. With Philip of Hesse, the Lutherans had a competent political strategist. At least for the time being, until all religious matters had been settled by a general council, the Protestants had reluctantly obtained recognition of their right to exist. Such a council was indeed convened by Pope Paul III – if only at the repeated insistence of the emperor – but there was little sign that the Protestant states would submit. In 1545, Charles decided to go to war. He found a pretext in the capture of the Duke of Brunswick-Wolfenbüttel by Lutheran princes, Catholics who had tried to reconquer the lands from which he had been expelled by his Lutheran subjects. Claiming that this capture violated imperial law, Charles opened the conflict in 1546, in which he was accompanied by Moritz, Duke of Saxony, an ambitious Lutheran prince to whom Charles had secretly promised the Saxon electorate.
The next war was divided into two phases, of which the emperor was victorious at the Battle of Mühlberg in 1547. Charles took advantage of this strong position and, in 1548, forced the estates to accept a provisional religious arrangement on the emperor`s terms.