Nor is there any sign that Elizabeth had resolved on a defiance of the Papacy. She was firm indeed to assert her father's claim of supremacy over the clergy and her own title to the throne. But the difficulties in the way of an accommodation on these points were such as could be settled by negotiation; and, acting on Cecil's counsel, Elizabeth announced her accession to the Pope. The announcement showed her purpose of making no violent break in the relations of England with the Papal See. But between Elizabeth and the Papacy lay the fatal question of the Divorce. To acknowledge the young Queen was not only to own her mother's marriage, but to cancel the solemn judgment of the Holy See in Catharine's favor and its solemn assertion of her own bastardy. The temper of Paul the Fourth took fire at the news. He reproached Elizabeth with her presumption in ascending the throne, recalled the Papal judgment which pronounced her illegitimate, and summoned her to submit her claims to his tribunal. Much of this indignation was no doubt merely diplomatic. If the Pope listened to the claims of Mary Stuart, which were urged on him by the French Court, it was probably only with the purpose of using them to bring pressure to bear on Elizabeth and on the stubborn country which still refused to restore its lands to the Church and to make the complete submission which Paul demanded. But Cecil and the Queen knew that, even had they been willing to pay such a price for the crown, it was beyond their power to bring England to pay it. The form too in which Paul had couched his answer admitted of no compromise. The summons to submit the Queen's claim of succession to the judgment of Rome produced its old effect. Elizabeth was driven, as Henry had been driven, to assert the right of the nation to decide on questions which affected its very life. A Parliament which met in January, 1559, acknowledged the legitimacy of Elizabeth and her title to the crown.

Such an acknowledgment in the teeth of the Papal repudiation of Anne Boleyn's marriage carried with it a repudiation of the supremacy of the Papacy. It was in vain that the clergy in convocation unanimously adopted five articles which affirmed their faith in transubstantiation, their acceptance of the supreme authority of the Popes as "Christ's vicars and supreme rulers of the Church," and their resolve "that the authority in all matters of faith and discipline belongs and ought to belong only to the pastors of the Church, and not to laymen." It was in vain that the bishops unanimously opposed the Bill for restoring the royal supremacy when it was brought before the Lords. The "ancient jurisdiction of the Crown over the Estate ecclesiastical and spiritual" was restored; the Acts which under Mary re-established the independent jurisdiction and legislation of the Church were repealed; and the clergy were called on to swear to the supremacy of the Crown and to abjure all foreign authority and jurisdiction. Further Elizabeth had no personal wish to go. A third of the Council and at least two-thirds of the people were as opposed to any radical changes in religion as the Queen. Among the gentry the older and wealthier were on the conservative side, and only the younger and meaner on the other. In the Parliament itself Sir Thomas White protested that "it was unjust that a religion begun in such a miraculous way and established by such grave men should be abolished by a set of beardless boys." Yet even this "beardless" parliament had shown a strong conservatism. The Bill which re-established the royal supremacy met with violent opposition in the Commons, and only passed through Cecil's adroit maneuvering.

But the steps which Elizabeth had taken made it necessary to go further. If the Protestants were the less numerous, they were the abler and the more vigorous party, and the break with Rome threw Elizabeth, whether she would or no, on their support. It was a support that could only be bought by theological concessions, and above all by the surrender of the Mass; for to every Protestant the Mass was identified with the fires of Smithfield, while the Prayer-book which it had displaced was hallowed by the memories of the Martyrs. The pressure of the reforming party indeed would have been fruitless had the Queen still been hampered by danger from France. Fortunately for their cause the treaty of Cateau Cambresis at this juncture freed Elizabeth's hands. By this treaty, which was practically concluded in March, 1559, Calais was left in French holding on the illusory pledge of its restoration to England eight years later; but peace was secured and the danger of a war of succession, in which Mary Stuart would be backed by the arms of France, for a while averted. Secure from without, Elizabeth could venture to buy the support of the Protestants within her realm by the restoration of the English Prayer-book. Such a measure was far indeed from being meant as an open break with Catholicism. The use of the vulgar tongue in public worship was still popular with a large part of the Catholic world; and the Queen did her best by the alterations she made in Edward's Prayer-book to strip it of its more Protestant tone. To the bulk of the people the book must have seemed merely a rendering of the old service in their own tongue. As the English Catholics afterward represented at Rome when excusing their own use of it, the Prayer-book "contained neither impiety nor false doctrine; its prayers were those of the Catholic Church, altered only so far as to omit the merits and intercession of the saints." On such concession as this the Queen felt it safe to venture in spite of the stubborn opposition of the spiritual estate. She ordered a disputation to be held in Westminster Abbey before the Houses on the question, and when the disputation ended in the refusal of the bishops to proceed an Act of Uniformity, which was passed in spite of their strenuous opposition, restored at the close of April the last Prayer-book of Edward, and enforced its use on the clergy on pain of deprivation.

At Rome the news of these changes stirred a fiercer wrath in Paul the Fourth, and his threats of excommunication were only held in check by the protests of Philip. The policy of the Spanish King still bound him to Elizabeth's cause, for the claims of Mary Stuart had been reserved in the treaty of Cateau Cambresis, and the refusal of France to abandon them held Spain to its alliance with the Queen. Vexed as he was at the news of the Acts which re-established the supremacy, Philip ordered his ambassador to assure Elizabeth he was as sure a friend as ever, and to soothe the resentment of the English Catholics if it threatened to break out into revolt. He showed the same temper in his protest against action at Rome. Paul had however resolved to carry out his threats when his death and the interregnum which followed gave Elizabeth a fresh respite. His successor, Pius the Fourth, was of milder temper and leaned rather to a policy of conciliation. Decisive indeed as the Queen's action may seem in modern eyes, it was far from being held as decisive at the time. The Act of Supremacy might be regarded as having been forced upon Elizabeth by Paul's repudiation of her title to the crown. The alterations which were made by the Queen's authority in the Prayer-book showed a wish to conciliate those who clung to the older faith. It was clear that Elizabeth had no mind merely to restore the system of the Protectorate. She set up again the royal supremacy, but she dropped the words "Head of the Church" from the royal title. The forty-two Articles of Protestant doctrine which Cranmer had drawn up were left in abeyance. If the Queen had had her will, she would have retained the celibacy of the clergy and restored the use of crucifixes in the churches.