His liberal tendencies led to conflict with traditionalist clergy in general and the supporters of Tractarianism during the years he taught at the University of Oxford (1829–1846) which coincided with a period of rapid social change and heightened political tensions.

His support for the campaign for the admission of non-Anglicans to the Universities of Cambridge and Oxford was unpopular at the time (1834) and led to serious protests when he was nominated to the Regius Professorship of Divinity two years later.

Election to these fellowships was by special examination intended to select the best possible minds and Hampden became a member of the group known as the "Noetics" who were Whigs in politics and freely critical of traditional religious orthodoxy.

Hampden was chosen to deliver the prestigious Bampton Lectures for 1832, in which he attempted to disentangle the original truth of Christianity from later accretions and superstitions, particularly scholastic philosophy.

[5] At the time, some thought he had committed himself to a heretical view of the Trinity akin to Socinianism and Sabellianism,[6] but serious questioning only started after the publication of his Observations on Religious Dissent in 1834, and wide-ranging outrage was sparked in 1836 after his nomination to the Regius Professorship of Divinity.

Hampden entered the public arena in August by publishing Observations on Religious Dissent in support of the admission of non-Anglicans to Oxford University on the strength of a simple declaration of faith.

[17] Even so, urged by the Duke of Wellington (recently elected Chancellor), on 10 November the heads of the Oxford Colleges recognised that public feeling was opposed to making schoolboys subscribe to the Articles on matriculation and by a single vote agreed to abolish the practice.

Hampden then produced a second edition of the pamphlet and sent a copy to John Henry Newman who, while recognising its "tone of piety" regretted that the arguments of the work tended "altogether to make shipwreck of the Christian faith".

[citation needed] In 1836 the Regius Professor of Divinity died suddenly and the Whig Prime Minister, Lord Melbourne, offered the post to Hampden.

As bishop of Hereford Dr Hampden made no change in his long-formed habits of studious seclusion, and though he showed no special ecclesiastical activity or zeal, the diocese certainly prospered in his charge.

Among the more important of his later writings were the articles on Aristotle, Plato and Socrates, which contributed to the eighth edition of the Encyclopædia Britannica, and afterwards reprinted with additions under the title of The Fathers of Greek Philosophy (Edinburgh, 1862).