This letter of Henry VIII. was clearly an ultimatum, non-compliance with which meant open war. At the beginning of 1531 steps were taken to prepare the way for royal supremacy. For exercising legatine powers in England Cardinal Wolsey had been indicted and found guilty of the violation of the stature of Praemunire, and as the clergy had submitted to his legatine authority they were charged as a body with being participators in his guilt. The attorney-general filed an information against them to the court of King's Bench, but when Convocation met it was intimated to the clergy that they might procure pardon for the offence by granting a large contribution to the royal treasury and by due submission to the king. The Convocation of Canterbury offered a sum of £100,000, but the offer was refused unless the clergy were prepared to recognise the king as the sole protector and supreme head of the church and clergy in England. To such a novel proposal Convocation showed itself decidedly hostile, but at last after many consultations had been held Warham, the aged Archbishop of Canterbury, proposed that they should acknowledge the king as "their singular protector only, and supreme lord, and as far as the law of Christ allows even supreme head." "Whoever is silent," said the archbishop, "may be taken to consent," and in this way by the silence of the assembly the new formula was passed.[19] At the Convocation of York, Bishop Tunstall of Durham, while agreeing to a money payment, made a spirited protest against the new title, to which protest Henry found it necessary to forward a reassuring reply. Parliament then ratified the pardon for which the clergy had paid so dearly, and to set at rest the fears of the laity a free pardon was issued to all those who had been involved in the guilt of the papal legate.

Clement VII. issued a brief in January 1531, forbidding Henry to marry again and warning the universities and the law courts against giving a decision in a case that had been reserved for the decision of the Holy See. When the case was opened at the Rota in the same month an excusator appeared to plead, but as he had no formal authority from the king he was not admitted. The case, however, was postponed from time to time in the hope that Henry might relent. In the meantime at the king's suggestion several deputations waited upon Catharine to induce her to recall her appeal to Rome. Annoyed by her obstinacy Henry sent her away from court, and separated from her her daughter. After November 1531, the king and queen never met again. Popular feeling in London and throughout England was running high against the divorce, and against any breach with the Emperor, who might close the Flemish markets to the English merchants. The clergy, who were indignant that their representatives should have paid such an immense sum to secure pardon for an offence of which they had not been more guilty than the king himself, remonstrated warmly against the taxation that had been levied on their revenues. Unmindful of the popular commotion, Henry proceeded to usurp the power of the Pope and of the bishops, and though he was outwardly stern in the repression of heresy, the friends of the Lutheran movement in England boasted publicly that the king was on their side.

When Parliament met again (Jan. 1532), the attacks on the clergy were renewed. A petition against the bishops, drawn up by Thomas Cromwell at the suggestion of Henry,[20] was presented in the name of the House of Commons to the king. In this petition the members were made to complain that the clergy enacted laws and statutes in Convocation without consulting the king or the Commons, that suitors were treated harshly before the ecclesiastical courts, that in regard to probates the people were worried by excessive fees and unnecessary delays, and that the number of holidays was injurious to trade and agriculture. This complaint was forwarded to Convocation for a reply. The bishops, while vindicating for the clergy the right to make their own laws and statutes, showed themselves not unwilling to accept a compromise, but Parliament at the instigation of Henry refused to accept their proposals. The king, who was determined to crush the power of the clergy, insisted that Convocation should abandon its right to make constitutions or ordinances without royal permission, and that the ordinances passed already should be submitted to a mixed commission appointed by the authority of the crown. Such proposals, so contrary to the customs of the realm and so destructive of the independence of the Church, could not fail to be extremely disagreeable to the bishops; but in face of the uncompromising attitude of the king they were forced to give way, and in a document known as the Submission of the Clergy they sacrificed the legislative rights of Convocation (May 1532). They agreed to enact no new canons, constitutions or ordinances without the king's consent, that those already passed should be submitted to a committee consisting of clergy and laymen nominated by the king, and that the laws adopted by this committee and approved by the king should continue in full force. Sir Thomas More, who had worked hard in defence of the Church, promptly resigned his office of Lord Chancellor that he might have a freer hand in the crisis that had arisen.