An answer to Dr. Stillingfleet's book of The unreasonableness of separation so far as it concerns The peaceable designe : with some animadversions upon the debate between him and Mr. Baxter concerning the national church and the head of it. (London : Thomas Parkhurst, 1682)

The foure wishes of Mr. John Humphrey,:in conclusion of his sermons printed 1653. Intituled An humble admission unto the Lord's Supper, &c. (London, 1654)

Free thoughts upon these heads : Of predestination, redemption, the salvability of the heathen, The Judaical Covenant, Justification, The Judge of Faith and the Scripture, Venial Sin, Of Liturgical and Conceived Prayer, Demonstrative Preaching, The Authority of the Laws of Men, The Power of the Magistrate about Religion, subjection to our present Queen. By John Humfrey, Born in Jan. 1620. and Aged now past 89 Years. (London : T. Parkhurst at the 3 Crowns in Cheapside and Jonathan Robinson at the Golden Lion in St. Paul's churchyard, and sold by J. Morphew near Stationers hall, 1710)

A letter to George Keith concerning the salvability of the heathen together with a testimony to the same doctrine, as long held and not newly taken up, out of several former books of him that writ it (London : The booksellers of London and Westminster, 1700)

The middle way of predetermination asserted. Between the Dominicans and Jesuites, Calvinists and Arminians, or, A scriptural enquiry into the influence and causation of God in and unto humane actions; expecially such as are sinfull. (London : Thomas Parkhurst, at the Bible and three Crowns at the lower end of Cheapside., 1679)

A plain, honest, easy and brief determination of the late controversy concerning that non-resistance of the higher powers .. (1710)