The aftermath of Essays and Reviews is a famous story (well told by Owen Chadwick in his The Victorian Church, 1972, vol. II, pp. 75–90) of muddled persecution. All that it made clear was that biblical criticism was neither a safe nor an honoured pursuit for clergymen. But before the book came out its contributors were known and suspect to the orthodox. Publication exposed them as a target.

Jowett had been in hot water five years before. In his commentary on Romans he had included an essay on the doctrine of atonement. He attacked the version of it, as morally objectionable as it was fraught with psychological melodrama, in which Christ's death was seen as a substitutionary propitiation of God's anger against sinful humanity. He was denounced to the Vice-Chancellor of Oxford and summoned to his study to re-subscribe to the Thirty-nine Articles. It was a ludicrous episode. But the indignity of it hurt him – as a Christian believer and as an eminent don who had just missed the Mastership of his college, Balliol. Also, his appointment as Professor of Greek in the preceding year (1854) had set off a tangled and humiliating train of events. Pusey, mingling decency with vindictiveness, attempted to get Jowett paid a proper salary so long as this could be dissociated from any apparent endorsement by the authorities of Jowett's views. That conundrum was not solved until 1865.