God a Good Master, 1641 (dedicated to Elizabeth Hampden, mother of John Hampden).
The Return of Mercies, 1641.
The Christian's Engagement, 1641.
Impedit ira animum, or Animadversions vpon . . . George Walker, 1641, (Walker's Defence, to which this is a reply, was published by Goodwin).
Impvtatio Fidei, or a Treatise on Justification, 1642. Later edited by John Wesley to combat Calvinist antinomianism.
The Butcher's Blessing, or the Bloody Intentions of Romish Cavaliers, 1642 (Jackson).
Innocencies Triumph, or an Answer to ... William Prynne, &c., 1644, (two editions same year, defends his 'Θεομαχία'). Innocency and Truth Triumphing, 1645, (continuation). Calumny Arraign'd, 1645, (answer to Prynne's reply).
A Vindication of Free Grace, 1645, (ed. by Samuel Lane, contains sermon 28 April 1644 by Goodwin, taken in shorthand by Thomas Rudyard).
Twelve . . . Serious Cautions, 1646.
Some Modest and Humble Queries, 1646 (Jackson).
Anapologesia Tes Antapologias, or The Inexcusablenesse of ... Antapologia, 1646 (first and only part; against Thomas Edwards).
A Candle to see the Sunne, 1647, (appendix to Hagiomastix). A Postscript ... to ... Hagiomastix, 1647.
Sion College Visited, or Animadversions on a Pamphlet of W. Jenkyns, 1647 (i.e. January 1648).
Nεοφυτοπρεβύτερος, or The Youngling Elder ... for the instruction of W. Jenkyn, 1648.
The Unrighteous Judge, 1648 (i.e. 18 January 1649), reply to Sir Francis Nethersole.
Truth's Conflict with Error, 1650, from shorthand report by John Weeks of disputations on universal redemption by Goodwin against Vavasor Powell, and John Simpson.
The Remedy of Unreasonableness, 1650 (Jackson).
Moses made Angry; a Letter ... to Dr. Hill, 1651 (Jackson).
Confidence Dismounted, or a Letter to Mr. Richard Resbury, 1651 (Jackson).
Εἰρηνομαχία, The Agreement and Distance of Brethren, 1652; 1671.
A Paraphrase, 1652; second edition with title An Exposition of the Ninth Chapter of the Epistle to the Romans, 1653 (dedicated to the Lord Mayor, John Fowke).
Philadelphia, or XL Queries, 1653, (on baptism).
Thirty Queries, 1653 (Jackson; on the magistrate's authority in religion). The Apologist Condemned, 1653 (Jackson, a vindication of this work).
Dissatisfaction Satisfied in Seventeen . . . Queries, 1654 (Jackson). Peace Protected, 1654, (amplification; contains a warning against the "fift monarchic" men).
A Fresh Discovery of the High Presbyterian Spirit, 1654, (controversy with six London booksellers, Thomas Underhill, Samuel Gellibrand, John Rothwell, Luke Fawne, Joshua Kirton, and Nathaniel Webb, who petitioned for the restraint of the press). The Six Booksellers Proctor Non-suited, 1655.
Mercy in her Exaltation, 1655, (funeral sermon, 20 April, for Daniel Taylor).
The Foot out of the Snare, 1656 (by John Toldervy, who had been a quaker; part by Goodwin).
Triumviri, or the Genius ... of ... Richard Resbury, John Pawson, and George Kendall, 1658.
Πλήρωμα τὰ Πνευματικόν, or a Being Filled with the Spirit, posthumous 1670, with recommendatory epistle by Ralph Venning; it is included in James Nichol's series of standard divines.
