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 However, the real flaw in the Emperor's plan was that he did not seek to reform the Diet, but left it standing, while a new organisation was introduced which was bound to come into conflict with existing institutions and could only supersede them after a long and wearisome constitutional struggle. Both its good points and its defects excited discontent. The territorial Princes feared to lose their hold over mediate lords when the latter would look not to them but to the League for protection; the cities dreaded the expense of having to keep internal and external peace in outlying lands like Burgundy and the Austrian Duchies. Bavaria had resolved to refuse, even if all the other Estates agreed; the College of Electors was unanimously hostile; the Diet as a whole disliked a measure which would bring its own authority into dispute, and Charles dropped the proposal without a struggle.

He was more fortunate in his reconstitution of the Reichskammer-gericht; he arrogated to himself the immediate nomination of its judges, reserved to his own Hofgericht questions of Church property and episcopal jurisdiction, and persuaded the Diet to adopt a codification of the principles by which the action of the Court should be governed, and to promise contributions for the Court's support. He was able to defy the remonstrances addressed to him on account of the Spanish troops, which, contrary to his election pledges, he had quartered in the Empire. He secured the establishment of a fund for the maintenance of internal and external peace, which was not, however, to be used without the Diet's consent; and obtained preferential treatment for the Netherlands by means of a perpetual treaty between them and the Empire. They were to contribute to national taxation but to be exempt from the national jurisdiction; they were thus partly removed from imperial control, though Germany was perpetually bound to the arduous task of their defence; the transfer of Utrecht and Gelders to the Burgundian circle was a mark of their incorporation in the Habsburg inheritance.

Meanwhile religion naturally occupied much of the attention of Charles and the Diet. The Emperor vowed that even when in the field against his enemies he had thought more about the Church than the war; and it was incumbent upon him to attempt some sort of solution at the Diet of Augsburg. The problem, difficult in any case, was rendered infinitely more so by his strained relations with the Pope; which the murder of Paul's son, Pierluigi Farnese, on September 10, 1547, with the suspected connivance of Ferrante di Gonzaga, the governor of Milan, of Granvelle, and even of Charles himself, did nothing to improve. The Pope was hardened in his determination not to let the Council leave Bologna. The Emperor obtained a unanimous recognition from the Estates to the effect that the prelates remaining at Trent constituted the only true Council. They also approved of Charles' refusal to publish the Tridentine decrees; and, going further than he desired, they demanded that Scripture, should be the test applied to all doctrines,