liament for the university, but was unseated on account of his orders. He served, however, as chairman of a committee of referees appointed by the Protector's council (14 July 1654) to devise means for the Christian composing of differences in the kirk of Scotland, and as one of the associates of the committees of toleration, and for the consideration of the proposals of Manasseh ben Israel (1654–5).
Owen retained the vice-chancellorship until 1658, when (9 Oct.) he was replaced by Dr. John Conant. In his execution of the office he displayed equal vigour and moderation. When the royalist rising was anticipated in the spring of 1654–5, he made himself responsible for the security of the town and county of Oxford, and was frequently to be seen riding at the head of a troop of horse, well mounted, and armed with sword and pistol. In defiance of academical etiquette, he dressed more like a layman than a divine, but was so far from slovenly that Anthony à Wood represents him as a fop; he was a strict disciplinarian, and curbed the license of the terræ filii by arresting one of them with his own hands and sending him to Bocardo (the university gaol). He fostered learning and piety, and discouraged persecution. He connived at the public use of the proscribed liturgy of the church of England in the house of Dr. Thomas Willis [q. v.], in the immediate vicinity of Christ Church; and to his influence it was mainly due that the Laudian professor of Arabic was secured in the possession of his Berkshire rectory [see Pocock, Edward].
Notwithstanding the heavy responsibilities which his various offices entailed, Owen found time to pass through the university press several elaborate theological treatises. In his ‘Diatriba de Divina Justitia seu Justitiæ Vindicatricis Vindiciæ’ (1653, 8vo) he attempted to cut the ground from under the feet of the Socinian by deducing the absolute necessity of satisfaction for sin from the constitution of the divine nature. He also plunged afresh into the Arminian controversy, opposing to John Goodwin's ‘Redemption Redeemed’ his ‘Doctrine of the Saints' Perseverance explained and confirmed,’ published in 1654 (fol.), with ‘Animadversions on Dr. H. Hammond's “Dissertationes Quatuor”’ (on the evidence for episcopacy afforded by the Ignatian epistles) [see Goodwin, John, and Hammond, Henry]. In 1655, at the request of the council of state, he entered the lists against John Biddle [q. v.] with ‘Vindiciæ Evangelicæ; or the Mystery of the Gospel vindicated and Socinianisme examined,’ 4to. This work brought Hammond into the field with a defence of the orthodoxy of Grotius, whom Owen had classed among Socinians. Owen replied in ‘A Review of the Annotations of Hugo Grotius in reference to the Doctrine of the Deity and Satisfaction of Christ; with a Defence of the Charge formerly laid against them’ (1656, 4to). To the same period belong several of his best known minor treatises—viz. ‘Of the Mortification of Sin in Believers,’ 1656, 8vo (2nd edit. 1658); ‘Of Communion with God the Father, Son, and Holy Ghost, each Person distinctly in Love, Grace, and Consolation,’ 1657, 4to, a piece of wire-drawn mysticism, severely criticised by William Sherlock [q. v.] in 1674 (cf. infra); ‘Of Schism: the true Nature of it discovered and considered with reference to the Present Differences in Religion,’ 1657, 8vo, an ingenious attempt to exonerate nonconformists from the guilt of schism, which provoked an answer from Daniel Cawdry [q. v.], to which Owen rejoined in ‘A Review of the True Nature of Schism,’ &c., 1657, 8vo; ‘Of Temptation: the Nature and Power of it,’ &c., 1658, 8vo; ‘Of the Divine Original, Authority, Self-evidencing Light and Power of the Scriptures,’ 1659, 8vo. Appended to this work were some ill-judged ‘Considerations on the Prolegomena and Appendix to the late Biblia Polyglotta,’ which drew from Brian Walton [q. v.] an animated reply; and ‘Some Exercitations’ (in Latin) against the quaker theory of inspiration, which were answered with unfriendly heat by Samuel Fisher in ‘Rusticus ad Academicos’ [see Fisher, Samuel, 1605–1665]. Owen attended the synod of independent divines held at the Savoy, 29 Sept. to 12 Oct. 1658, when the confession of faith known as the Savoy Declaration was formulated.
After the abdication of Richard Cromwell Owen was commissioned by the council of state to raise a volunteer corps for the defence of Oxford. During the critical period which ensued he was in London, straining every nerve to secure Monck's adhesion to the independent faction. Ejected from Christ Church on 13 March 1659–60, he returned to an estate which he had bought at Stadhampton, and while there published Θεολογούμενα παντοδαπά, an encyclopædic Latin treatise on the history of religion and theology, natural and revealed, from the creation to the reformation. While the bill for uniformity in the prayers and ceremonies of the church of England was pending, he tendered a temperate protest against it in ‘A Discourse concerning Liturgies and their Imposition,’ London, 1662, 8vo. This tract