He constantly preached at St. Mary's, wearing a 'velvet cassock,' and held a weekly meeting at his lodgings, on the plan of an independent church meeting, of which Stephen Charnock [q. v.] and Theophilus Gate [q. v.] were members. John Howe (1630–1705) [q. v.], then a student at Magdalen, being of presbyterian sentiments, 'did not offer to join' this meeting; Goodwin invited and admitted him 'upon catholic terms.' In the 'Spectator,' No. 494, 26 Sept. 1712, Addison gives an account of the examination of a student (either Anthony Henley [q. v.] or, according to Granger, Thomas Bradbury, not the divine) in grace rather than in grammar, by 'a very famous independent minister, who was head of a college in those times.' The reference is evidently to Goodwin; the 'half a dozen nightcaps upon his head' allude to the two double skull-caps shown in his portrait.
On 14 Aug. 1650 Goodwin was appointed on a commission (including Milton) to make an inventory of the records of the Westminster Assembly. In 1653 he was made a commissioner for the approbation of public preachers; and on 16 Dec. 1653 he was made D.D. of Oxford, being described in the register as 'in scriptis in re theologica quamplurimis orbi notus.' In 1654 he was one of the assistants to the commissioners of Oxfordshire for removing scandalous ministers. In 1658 Goodwin and his friends petitioned Cromwell for liberty to hold a synod and draw up a confession of faith. Cromwell gave an unwilling consent, but died (3 Sept.) before the time fixed for the opening of the assembly. Goodwin attended him on his deathbed. A few minutes before he expired Goodwin 'pretended to assure them in a prayer that he was not to die' (Burnet). A week later a fast-day was held at Whitehall; Tillotson, who was present, assured Burnet that in Goodwin's prayer the expression occurred, 'Thou hast deceived us, and we were deceived.' Burnet does not notice that this is a quotation (Jer. xx. 7).
Goodwin and his friends met at the Savoy for eleven or twelve days from 12 Oct. Representatives, mostly laymen, of over a hundred independent churches were present. Goodwin and John Owen were the leaders in a committee of six divines appointed to draw up a confession. They adopted, with a few verbal alterations, the doctrinal definitions of the Westminster confession, reconstructing only the part relating to church government. The main effect of the declaration of the Savoy assembly was to confirm the Westminster theology.
On 18 May 1660 Goodwin was deprived by the convention parliament of his office as president of Magdalen. He took to London several members of his Oxford church, and founded an independent congregation, since removed to Fetter Lane. His later years were spent in study. In the great fire of 1666 more than half his library, to the value of 500l., was burned; his divinity books were saved. He died of fever, after a short illness, on 23 Feb. 1680, and was buried in Bunhill Fields. The Latin epitaph for his tomb, written by Thomas Gilbert, B.D. [q. v.], was 'not suffer'd to be engrav'd' in full; it specifies his great knowledge of ecclesiastical antiquities. His portrait was engraved by R. White (1680); for Palmer's first edition it was engraved from the original painting by James Caldwall [q. v.]; for the second edition it was re-engraved by the elder William Holl [q. v.] His face, with its strong hooked nose and curling locks, has a Jewish cast. He married first, in 1638, Elizabeth, daughter of Alderman Prescott, by whom he had a daughter, married to John Mason of London; secondly, in 1649, Mary Hammond, then in her seventeenth year, by whom he had two sons, Thomas (see below) and Richard, who died on a voyage to the East Indies as one of the company's factors; and two daughters, who died in infancy.
Goodwin's sermons have much unction; his expositions are minute and diffuse; great historical value attaches to the defences of independency in which he was concerned. He began to publish sermons in 1636, and brought out a collection of them in 1645, 4to. To the seventh piece in this collection, 'The Heart of Christ in Heaven towards Sinners on Earth' (1643), a writer in the 'Edinburgh Review' (January 1874) has endeavoured, following Lemontey and Wenzelburger, to trace the suggestion of the modern Roman catholic devotion to the sacred heart; the supposed link with Goodwin being père Claude de la Colombière. Isaac Watts (Glory of Christ, 1747) had previously drawn attention to the unusual language of Goodwin 'in describing the glories due to the human nature' of our Lord. Of his writings the larger number were not printed in his lifetime, though prepared for the press. Five folio volumes of his works were edited by Thankful Owen, Thomas Baron, and Thomas Goodwin the younger, in 1682, 1683, 1692, 1697, and 1704; reprinted, 1861, 6 vols. 8vo; condensed by Babb, 1847-50, 4 vols. 8vo. Not included in the works are the following, in which he had a chief hand: 1 . 'An Apologeticall Narration hvmbly svbmitted to the honourablb [sic] Houses of Parliament,' &c., 1643, 4to. 2. 'The Reasons presented by the Dissenting Brethren,' &c., 1648, 4to