Hitherto Bonner had been known as a somewhat coarse and unscrupulous tool of Cromwell, a sort of ecclesiastical Wriothesley, He is not known to have protested against any of the changes effected by his masters; he professed to be no theologian, and was wont, when asked theological questions, to refer his interrogators to the divines. He had graduated in law, and not in theology. There was nothing in the Reformation to appeal to him, except the repudiation of papal control; and he was one of those numerous Englishmen whose views were faithfully reflected in the Six Articles. He became a staunch Conservative, and, apart from his embassy to the emperor in 1524–1543, was mainly occupied during the last years of Henry's reign in brandishing the “whip with six strings.”
The accession of Edward VI opened a fresh and more creditable chapter in Bonner's career. Like Gardiner, he could hardly repudiate that royal supremacy, in the establishment of which he had been so active an agent; but he began to doubt that supremacy when he saw to what uses it could be put by a Protestant council, and either he or Gardiner evolved the theory that the royal supremacy was in abeyance during a royal minority. The ground was skilfully chosen, but it was not legally nor constitutionally tenable. Both he and Gardiner had in fact sought fresh licences to exercise their ecclesiastical jurisdiction from the young king; and, if he was supreme enough to confer jurisdiction, he was supreme enough to issue the injunctions and order the visitation to which Bonner objected. Moreover, if a minority involved an abeyance of the royal supremacy in the ecclesiastical sphere, it must do the same in the temporal sphere, and there could be nothing but anarchy. It was on this question that Bonner came into conflict with Edward's government. He resisted the visitation of August 1547, and was committed to the Fleet; but he withdrew his opposition, and was released in time to take an active part against the government in the parliament of November 1547. In the next session, November 1548-March 1549, he was a leading opponent of the first Act of Uniformity and Book of Common Prayer. When these became law, he neglected to enforce them, and on the 1st of September 1549 he was required by the council to maintain at St Paul's Cross that the royal authority was as great as if the king were forty years of age. He failed to comply, and after a seven days' trial he was deprived of his bishopric by an ecclesiastical court over which Cranmer presided, and was sent to the Marshalsea. The fall of Somerset in the following month raised Bonner's hopes, and he appealed from Cranmer to the council. After a struggle the Protestant faction gained the upper hand, and on the 7th of February 1550 Bonner's deprivation was confirmed by the council sitting in the Star Chamber, and he was further condemned to perpetual imprisonment.
Because Edward VI died in 1553, that perpetual imprisonment did not last that long. He participated in the ecclesiastical investigations of heresy, but the Catholic Encyclopedia notes that the image of him as "Bloody Bonner", presented by Foxe and Bale, had been corrected in later centuries:
Even A.F. Pollard, a definite Whig historian, in the Encyclopedia Britannica tries to be more balanced in his view of Bishop Bonner:
On the other hand, Bonner did not go out of his way to persecute; many of his victims were forced upon him by the council, which sometimes thought that he had not been severe enough (see Acts of the P.C. 1554–1556, pp. 115, 139; 1556–1558, pp. 18, 19, 216, 276). So completely had the state dominated the church that religious persecutions had become state persecutions, and Bonner was acting as an ecclesiastical sheriff in the most refractory district of the realm. Even Foxe records instances in which Bonner failed to persecute. But he had no mercy for a fallen foe; and he is seen at his worst in his brutal jeers at Cranmer, when he was entrusted with the duty of degrading his former chief. It is a more remarkable fact that, in spite of his prominence, neither Henry VIII. nor Mary should ever have admitted him to the privy council. He seems to have been regarded by his own party as a useful instrument, especially in disagreeable work, rather than as a desirable colleague.
Pollard describes Bonner's last years:
On her accession Elizabeth refused to allow him to kiss her hand; but he sat and voted in the parliament and convocation of 1559. In May he refused to take the oath of supremacy, acquiring like his colleagues consistency with old age. He was sent to the Marshalsea, and a few years later was indicted on a charge of praemunire on refusing the oath when tendered him by his diocesan, Bishop Horne of Winchester. He challenged the legality of Horne's consecration, and a special act of parliament was passed to meet the point, while the charge against Bonner was withdrawn. He died in the Marshalsea on the 5th of September 1569, and was buried in St George's, Southwark, at midnight to avoid the risk of a hostile demonstration.