Continental reformer Philipp Melanchthon was aware that he was very much admired by Henry. In early 1539, Melanchthon wrote several letters to Henry criticising his views on religion, in particular his support of clerical celibacy. By late April another delegation from the Lutheran princes arrived to build on Melanchthon's exhortations. Cromwell wrote a letter to the king in support of the new Lutheran mission. The king had begun to change his stance and concentrated on wooing conservative opinion in England rather than reaching out to the Lutherans. On 28 April 1539, Parliament met for the first time in three years. Cranmer was present, but Cromwell was unable to attend due to ill health. On 5 May the House of Lords created a committee with the customary religious balance between conservatives and reformers to examine and determine doctrine. The committee was given little time to do the detailed work needed for a thorough revision. On 16 May, the Duke of Norfolk noted that the committee had not agreed on anything, and proposed that the Lords examine six doctrinal questions—which eventually formed the basis of the Six Articles. They affirmed the conservative interpretation of doctrines such as the real presence, clerical celibacy, and the necessity of auricular confession, the private confession of sins to a priest. As the Act of the Six Articles neared passage in Parliament, Cranmer moved his wife and children out of England to safety. Up until this time, the family was kept quietly hidden, most likely in Ford Palace in Kent. The Act passed Parliament at the end of June and it forced Latimer and Nicholas Shaxton to resign their dioceses given their outspoken opposition to the measure.
The setback for the reformers was short-lived. By September, Henry was displeased with the results of the Act and its promulgators; the ever-loyal Cranmer and Cromwell were back in favour. The king asked his archbishop to write a new preface for the Great Bible, an English translation of the Bible that was first published in April 1539 under the direction of Cromwell. The preface was in the form of a sermon addressed to readers. As for Cromwell, he was delighted that his plan of a royal marriage between Henry and Anne of Cleves, the sister of a German prince was accepted by the king. In Cromwell's view, the marriage could potentially bring back contacts with the Schmalkaldic League. Henry was dismayed with Anne when they first met on 1 January 1540 but married her reluctantly on 6 January in a ceremony officiated by Cranmer. The marriage ended in disaster as Henry decided that he would request a royal divorce. This resulted in Henry being placed in an embarrassing position and Cromwell suffered the consequences. His old enemies, including the Duke of Norfolk, took advantage of the weakened Cromwell and he was arrested on 10 June. He immediately lost the support of all his friends, including Cranmer. As Cranmer had done for Anne Boleyn, he wrote a letter to the king defending the past work of Cromwell. Henry's marriage to Anne of Cleves was quickly annulled on 9 July by the vice-gerential synod, now led by Cranmer and Gardiner.
Cranmer's family had been exiled to the Continent in 1539. It is not known exactly when they returned to England, but it was soon after the accession of Edward VI in 1547 that Cranmer publicly acknowledged their existence. Not much is known about the early years of the children. His daughter, Margaret, was likely born in the 1530s and his son, Thomas, came later, probably during the reign of Edward. Around the time of Mary's accession, Cranmer's wife, Margarete, escaped to Germany, while his son was entrusted to his brother, Edmund Cranmer, who took him to the Continent. Margarete Cranmer eventually married Cranmer's favourite publisher, Edward Whitchurch. The couple returned to England after Mary's reign and settled in Surrey. Whitchurch also negotiated for the marriage of Margaret to Thomas Norton. Whitchurch died in 1562 and Margarete married for the third time to Bartholomew Scott. She died in the 1570s. Both of Cranmer's children died without issue and his line became extinct.