Archdeacon (afterwards Cardinal) Manning; and some of the seceders strove to show that Pusey was guilty of cowardice and inconsistency in not following their example. At the same moment, too, the second set of clergy whom Pusey had sent to the church he had built at Leeds followed in the steps of the first vicar, the Rev. Richard Ward, and went over to Rome. The so-called ‘Papal aggression’ of 1850 intensified the hatred felt for the party which Pusey represented. This year was perhaps the most clouded in the whole of his life. Blomfield, bishop of London, openly attacked him in a charge to his clergy, and Bishop Wilberforce (of Oxford) secretly inhibited him from preaching in his diocese. He defended himself against aspersions on his character in private and public letters, especially in his ‘Letter to the Bishop of London,’ written in 1850. But while he declined to make any declaration against the church of Rome, he asserted at a public meeting that it was his intention to die in the bosom of the church of England. Such an utterance reassured many wavering friends, and did not a little to stay the steps of intending seceders. In 1856, when Archdeacon Denison was charged with holding heretical views on the doctrine of the holy eucharist, Pusey published, by way of supporting him, ‘The Doctrine of the Real Presence, as contained in the Fathers, from the death of St. John the Evangelist to the fourth General Council, vindicated in Notes on a Sermon, “The Presence of Christ in the Holy Eucharist,” preached A.D. 1853 before the University of Oxford.’ This appendix to a sermon is a volume of upwards of seven hundred pages, containing not only quotations from the fathers, but also a large mass of other information on the doctrine of the holy eucharist. A supplement was issued in 1857, when the trial had been decided in the archdeacon's favour, entitled ‘The Real Presence of the Body and Blood of our Lord Jesus Christ, the Doctrine of the English Church.’
Pusey's work in the tractarian movement had aimed at the strengthening of the church of England by the restoration of those portions of the teaching of the church which for some years had been overlooked. The opposition of earnest low churchmen to the ‘Oxford movement’ had, in his opinion, encouraged the growth of latitudinarianism, the possibility of which he had foreseen since he had studied in Germany. He therefore turned in later life from the war on behalf of tractarianism to engage in conflict with the latitudinarian tendency. The struggle first centred round the reform of the university. The first royal university commission had recommended many changes which were unwelcome to a large body of the resident members of the university. In the agitation which followed the publication of their report in 1852, Pusey was the selected champion of the old order of things. The heads of houses issued a report in reply to that of the commissioners, and at the head of the volume they placed Pusey's evidence on the proposed changes. It is a lengthy and learned defence of the tutorial system of the English universities, and of clerical influence in the training of young men, as against the scheme for increasing the professoriate and diminishing the number of clerical tutorships. He followed up the subject in 1854 in a defence of his evidence, entitled ‘Collegiate and Professorial Teaching and Discipline,’ in which he insisted on the training of the moral and religious nature as the true object of the universities, with and through the discipline of the intellect; and he maintained that it would be a perversion of a university to turn it into ‘a forcing-house for intellect.’ When the act, based on the recommendation of the commission, had passed, Pusey was at once elected to the new hebdomadal council which, under this act, displaced the old board of heads of houses. In this council he retained a prominent place until he was compelled to resign it by old age. Pusey fought the battle of the church in council and convocation; but it was throughout a losing cause. The constitution of the university was steadily altered according to the will of the liberal party; but Pusey's opposition at least secured a breathing-space for the church to prepare for the altered conditions of its life in Oxford.
A more direct conflict with latitudinarian teaching followed. Pusey had preached several times in the university pulpit directly in defence of the faith, especially two striking sermons, in 1855, on the ‘Nature of Faith in relation to Reason.’ The notes to these sermons made it clear that he regarded the undogmatic theological teaching of the regius professor of Greek, Benjamin Jowett, as a serious danger to the youth of Oxford. When, therefore, a proposal was brought before the university that the very inadequate stipend of that professorship should be increased, Pusey felt bound to oppose it. He feared that acceptance of such a proposal would be understood to express approval of the teaching of the holder of the Greek chair. Eventually, to justify this opposition, he endeavoured to do for Jowett what he repeatedly desired to have done in his own case. He attempted to submit the doctrinal question to the decision of a court of law. Accordingly, in