He was educated at Broadgates Hall, now Pembroke College, Oxford, graduating bachelor of civil and canon law in June 1519. He was ordained about the same time, and admitted doctor of civil law (DCL) in 1525.
During the following years he was much employed on important embassies in the king's interests, first to the pope to appeal against the excommunication pronounced in July 1533, afterwards to the Emperor to dissuade him from attending the general council which the pope wished to summon at Vicenza. Towards the end of 1535 he was sent to further what he called "the cause of the Gospel" (Letters and Papers, 1536, No. 469) in North Germany; and in 1536 he wrote a preface to Stephen Gardiner's De vera Obedientia, which asserted the royal and denied the papal supremacy, and was received with delight by the Lutherans. After a brief embassy to the Emperor in the spring of 1538, Bonner succeeded Gardiner as ambassador to the French Court in Paris. In this capacity he proved capable and successful, though irritation was frequently caused by his overbearing and dictatorial manner. He began his mission by sending Cromwell a long list of accusations against his predecessor. He was almost as bitter against Wyatt and Mason, whom he denounced as a "papist," and the violence of his conduct led Francis I to threaten him with a hundred strokes of the halberd. He seems, however, to have pleased his patron, Cromwell, and perhaps Henry, by his energy in seeing the king's "Great" Bible in English through the press in Paris. He was already king's chaplain; his appointment at Paris had been accompanied by promotion to the See of Hereford (November 27 1538) but owing to his absence he could neither be consecrated nor take possession of his see, and he was still abroad when he was translated to the Bishopric of London (October, 1539). Bonner returned to England and was consecrated April 4, 1540.
Hitherto Bonner had had a reputation 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 in the habit, when asked technical questions, to refer his interrogators to the theologians. 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 Henry's Act of the Six Articles. Indeed, almost his first duty as Bishop of London was to try heretics under these articles; accusations of excessive cruelty and bias against the accused were spread broadcast by his enemies, and from the first he seems to have been unpopular in London. He became a staunch conservative. During the years 1542-43 he was again abroad in Spain and Germany as ambassador to the emperor, at the end of which time he returned to London.
The death of the king on January 28 1547, proved the turning point in Bonner's career. Hitherto he had shown himself entirely subservient to the sovereign, supporting him in the matter of the divorce, approving of the suppression of the religious houses, taking the oath of Supremacy which Fisher and More refused at the cost of life itself. But while accepting the schism from Rome, he had always resisted the innovations of the Reformers, and held to the doctrines of the old religion. Therefore from the first he put himself in opposition to the religious changes introduced by Protector Somerset and Archbishop Cranmer. Bonner 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 skillfully 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 Edward VI; 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. It was on this question that he came into conflict with Edward's government.
Bonner was at once restored to his see, his deprivation being regarded as invalid and Ridley as an intruder. He vigorously restored Roman Catholicism in his diocese, made no difficulty about submitting to the papal jurisdiction which he had foresworn. During 1554 Bonner carried out a visitation of his diocese, restoring the Mass and the manifold practices and emblems of Catholic life, but the work was carried out slowly and with difficulty. To help in the work, Bonner published a list of thirty-seven "Articles to be enquired of", but these led to such disturbances that they were temporarily withdrawn.
There was in London at this time a determined Reforming element which opposed in every way the restoration of Catholic worship; although the Parliament in 1554 welcomed Pole as Papal Legate and sought absolution and reconciliation from him with apparent unanimity, there was a real hostility to the whole proceeding among a boisterous section of the populace. Street brawls arising out of religious disputes were frequent, and Bonner himself was physically attacked on at least two occasions.
Mary's administration thought that the Reformers would best be dealt with by the ecclesiastical tribunals, rather than by the civil power, and on Bonner, as Bishop of London, fell the chief burden to stamp out religious dissent. Therefore, in 1555 began the persecution to which he owes his notoriety among his detractors as Bloody Bonner. Besides his judicial work in his own diocese, Bonner was appointed to degrade Cranmer at Oxford in February 1556. The part he took in these affairs gave rise to intense hatred on the part of the rebels. Foxe in his "Book of Martyrs" summed up this view in two lines:
His apologists, including defenders of Catholicism in England, contend that his action was merely "official", and that "he had no control" over the fate of the accused "once they were declared to be irreclaimable heretics and handed over to the secular power; but he always strove by gentle suasion first to reconcile them to the Church" (Mr Gairdner, qtd in Catholic Encyclopedia). The Catholic Encyclopedia estimates the number of persons executed as heretics in his jurisdiction as about 120, rather than 300. Bonner did not go out of his way to persecute; many of his victims were forced upon him by the king and queen in Council, which at one point addressed a letter to Bonner on the express ground that he was not proceeding with sufficient severity. 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 John Foxe records instances in which Bonner failed to persecute.
Bonner's detractors, beginning with his Protestant contemporaries John Foxe and John Bale and continuing through most English historiography of the period, paint a different picture. Bonner, they point out, was one of those who brought it to pass that the condemnation of heretics to the fire should be part of his ordinary official duties, and he was represented as hounding men and women to death with merciless vindictiveness. Cuthbert Tunstall, Bishop of Durham, was as loyal a Roman Catholic as Bonner, but he left a different reputation behind him. Bale, formerly a friar and ex-Bishop of Ossory, published from his place of exile at Basle in 1554, an attack on the bishop, in which he speaks of him as "the bloody sheep-bite of London", "bloody Bonner", and still coarser epithets. Bonner is seen at his worst, by many critics, in his brutal jeers at Cranmer, his former superior. Others contend 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.
Bonner's most important writings date from this time. They include Responsum et Exhortatio in laudem Sacerdotii (1553); Articles to be enquired of in the General Visitation of Edmund Bishop of London (1554); and Homelies sette forth by Eddmune Byshop of London, . . . to be read within his diocese of London of all Parsons, vycars and curates, unto their parishioners upon Sondayes and holy days (1555). There was also published under his name a catechism, probably written by his chaplains, Nicholas Harpsfield and Henry Pendleton, entitled "A profitable and necessary doctrine" (1554, 2d ed. 1555).
A more charitable assessment of Bonner's character was made by an Anglican historian, S.R. Maitland, who considers him,
"a man, straightforward and hearty, familiar and humorous, sometimes rough, perhaps coarse, naturally hot tempered, but obviously (by the testimony of his enemies) placable and easily intreated, capable of bearing most patiently much intemperate and insolent language, much reviling and low abuse directed against himself personally, against his order, and against those peculiar doctrines and practices of his church for maintaining which he had himself suffered the loss of all things, and borne long imprisonment. [...] In short, we can scarcely read with attention any one of the cases detailed by those who were no friends of Bonner, without seeing in him a judge who (even if we grant that he was dispensing bad laws badly) was obviously desirous to save the prisoner's life."
This verdict was generally followed by later historians. Lord Acton in the Cambridge Modern History (1903) argued: "The number of those put to death in his diocese of London was undoubtedly disproportionately large, but this would seem to have been more the result of the strength of the reforming element in the capital and in Essex than of the employment of exceptional rigor; while the evidence also shows that he himself patiently dealt with many of the Protestants, and did his best to induce them to renounce what he conscientiously believed to be their errors."
Bonner's Homelies to be read within his diocese of London of all Parsons, vycars and curates (1555) were translated into Cornish by John Tregear, and are now the largest single work of traditional Cornish prose.
His name lives on in folk memory in Norfolk where ladybirds are named bishibarnabees (Bishop Bonner's bee) perhaps after their ecclesiastical colouring, or, more likely, the association of red and black with blood and death. Just so, Bonner will be forever remembered as "Bloody Bonner".