Anthony Sadler (3 July 1654) has often been quoted from Sadler's account, but this should be compared with the pamphlet in reply [see Nye, John, d. 1688]. The ‘instrument of government’ had proposed to tolerate all Christians; the parliament which met September 1654 interpreted this to mean all who held the ‘fundamentals.’ Nye was put on a committee to define ‘fundamentals;’ their plans were upset by Baxter; they drew up and printed (1654, 4to) a list of sixteen ‘principles of faith,’ but the document was shelved on the dissolution of parliament (22 Jan. 1655). Some time in 1654 Nye received the rectory of St. Bartholomew, Exchange, vacant by the sequestration of John Grant, D.D.; he was succeeded at Acton by Thomas Elford, an independent. In 1656 Baxter approached Nye with a view to terms of accommodation with independents; the irreducible difference was in regard to ordination. Nye took part in the Savoy conference of October 1658, when the Westminster confession was raised in the independent sense, and signed the remarkable preface to the ‘declaration of faith and order’ (1659) written by John Owen, D.D. (1616–1683) [q. v.] It seems clear that at the Wallingford House meetings, early in 1659, he acted in the republican interest. He strongly opposed the measure reimposing the covenant on 5 March 1660.
At the Restoration he lost his preferments, and narrowly escaped exclusion from the indemnity, on condition of never again holding civil or ecclesiastical office. He printed an exculpatory pamphlet, addressed to the Convention parliament; in this he says he had been a preacher forty years, and was now in the sixty-fifth year of his age. In January 1661 he signed the ‘declaration of the ministers of congregational churches’ against the rising of the Fifth-monarchy men under Venner. His papers connected with the commission of ‘triers’ were ordered (7 Jan. 1662) to be deposited in Juxon's care at Lambeth. On the appearance of Charles II's abortive declaration of indulgence (26 Dec. 1662), Nye and other independents waited on the king. Nye fell back on Bradshaw's doctrine of the royal supremacy in church and state, and upheld the king's prerogative of dispensing with ecclesiastical laws. He went to Baxter (2 Jan. 1663), urging him to take the lead in an address of thanks; but Baxter had burned his fingers, and would ‘meddle no more in such matters;’ all his party objected to any toleration that would include papists. Nye left London. In 1666, however, after the fire, he returned and preached in open conventicles. On the indulgence of 1672, he ministered to an independent church in Cutlers' Hall, Cloak Lane, Queen Street, of which he was ‘doctor,’ the pastor being John Loder (d. 30 Dec. 1673), who had been his assistant at St. Bartholomew's, Exchange.
Nye died at ‘Brompton in the parish of Kensington,’ in September 1672, and was buried in St. Michael's, Cornhill, on 27 Sept. His wife, Judith, survived him, and probably died in 1680. After her death, his eldest son Henry, applied (2 Oct. 1680) for letters of administration to his father's estate, which were granted on 13 Oct. 1681; he subsequently edited some of his father's papers. John (d. 1688), the second son, is separately noticed. Rupert, the third son, matriculated from Magdalen College, Oxford, on 25 Oct. 1659, and died in 1660. Judith, his daughter, was buried in 1670 at Kensington.
Calamy describes Nye as ‘a man of uncommon depth.’ He and his fellow independents, John Goodwin [q. v.], and Peter Sterry [q. v.], were the most original minds among the later puritans. His literary remains, ephemeral pamphlets, are suggestive of the subtle powers which impressed his contemporaries. He was reckoned a schemer; Lilly, against whose astrology he had preached, calls him ‘jesuitical.’ Howe said he was a man who must be consulted, or he would know what was going on, and ‘if he disliked, would hinder it.’ But he had no vulgar ambitions; he sought no personal popularity; the accusation of enriching himself is groundless. Butler has made merry with his ‘thanksgiving beard;’ he ‘did wear a tail upon his throat.’ He held the curious view that, at sermons, the preacher should wear his hat, the audience being uncovered; at sacraments the minister should be bareheaded and the communicants covered.
He published: 1. ‘Letter from Scotland,’ &c., 1643, 4to (written by Nye, signed also by Marshall). 2. ‘Exhortation to the Taking of the Solemn League and Covenant,’ &c., 1643 [1644], 4to; several reprints (that of 1660, 4to, called ‘second edition,’ was brought out by opponents in consequence of No. 3). 3. ‘Beames of former Light, discovering how evil it is to impose … Formes,’ &c., 1660, 4to; another edition, 1660, 8vo. Posthumous were: 4. ‘The Case of Philip Nye, Minister, humbly tendered to the consideration of the Parliament,’ &c. [1660], 4to. 5. ‘Sermon at the Election of the Lord Mayor,’ &c., 1661, 4to. 6. ‘Case of great and present Use,’ &c., 1677, 8vo. 7. ‘The Lawfulness of the Oath of Supremacy,’ &c.; appended are ‘Vindication of Dissenters,’ &c., and ‘Some Account of …