As has been said, Bunyan's pen was almost idle during the last six years of his imprisonment. Only two of his works were produced in this period: his "Confession of Faith," and his "Defence of the Doctrine of Justification by Faith." Both were written very near the end of his prison life, and published in the same year, 1672, only a week or two before his release. The object of the former work was, as Dr. Brown tells us, "to vindicate his teaching, and if possible, to secure his liberty." Writing as one "in bonds for the Gospel," his professed principles, he asserts, are "faith, and holiness springing therefrom, with an endeavour so far as in him lies to be at peace with all men." He is ready to hold communion with all whose principles are the same; with all whom he can reckon as children of God. With these he will not quarrel about "things that are circumstantial," such as water baptism, which he regards as something quite indifferent, men being "neither the better for having it, nor the worse for having it not." "He will receive them in the Lord as becometh saints. If they will not have communion with him, the neglect is theirs not his. But with the openly profane and ungodly, though, poor people! they have been christened and take the communion, he will have no communion. It would be a strange community, he says, that consisted of men and beasts. Men do not receive their horse or their dog to their table; they put them in a room by themselves." As regards forms and ceremonies, he "cannot allow his soul to be governed in its approach to God by the superstitious inventions of this world. He is content to stay in prison even till the moss grows on his eyelids rather than thus make of his conscience a continual butchery and slaughter-shop by putting out his eyes and committing himself to the blind to lead him. Eleven years' imprisonment was a weighty argument to pause and pause again over the foundation of the principles for which he had thus suffered. Those principles he had asserted at his trial, and in the tedious tract of time since then he had in cold blood examined them by the Word of God and found them good; nor could he dare to revolt from or deny them on pain of eternal damnation."

The second-named work, the "Defence of the Doctrine of Justification by Faith," is entirely controversial. The Rev. Edward Fowler, afterwards Bishop of Gloucester, then Rector of Northill, had published in the early part of 1671, a book entitled "The Design of Christianity." A copy having found its way into Bunyan's hands, he was so deeply stirred by what he deemed its subversion of the true foundation of Evangelical religion that he took up his pen and in the space of six weeks composed a long and elaborate examination of the book, chapter by chapter, and a confutation of its teaching. Fowler's doctrines as Bunyan understood them - or rather misunderstood them - awoke the worst side of his impetuous nature. His vituperation of the author and his book is coarse and unmeasured. He roundly charges Fowler with having "closely, privily, and devilishly turned the grace of God into a licentious doctrine, bespattering it with giving liberty to lasciviousness;" and he calls him "a pretended minister of the Word," who, in "his cursed blasphemous book vilely exposes to public view the rottenness of his heart, in principle diametrically opposite to the simplicity of the Gospel of Christ, a glorious latitudinarian that can, as to religion, turn and twist like an eel on the angle, or rather like the weathercock that stands on the steeple;" and describes him as "contradicting the wholesome doctrine of the Church of England." He "knows him not by face much less his personal practise." He may have "kept himself clear of the ignorant Sir Johns who had for a long time, as a judgment of God, been made the mouth to the people - men of debauched lives who for the love of filthy lucre and the pampering of their idle carcases had made shipwreck of their former faith;" but he does know that having been ejected as a Nonconformist in 1662, he had afterwards gone over to the winning side, and he fears that "such an unstable weathercock spirit as he had manifested would stumble the work and give advantage to the adversary to speak vilifyingly of religion." No excuse can be offered for the coarse violence of Bunyan's language in this book; but it was too much the habit of the time to load a theological opponent with vituperation, to push his assertions to the furthest extreme, and make the most unwarrantable deductions from them. It must be acknowledged that Bunyan does not treat Fowler and his doctrines with fairness, and that, if the latter may be thought to depreciate unduly the sacrifice of the Death of Christ as an expiation for man's guilt, and to lay too great a stress on the moral faculties remaining in the soul after the Fall, Bunyan errs still more widely on the other side in asserting the absolute, irredeemable corruption of human nature, leaving nothing for grace to work upon, but demanding an absolutely fresh creation, not a revivification of the Divine nature grievously marred but not annihilated by Adam's sin.

A reply to Bunyan's severe strictures was not slow to appear. The book bears the title, characteristic of the tone and language of its contents, of "DIRT WIP'T OFF; or, a manifest discovery of the Gross Ignorance, Erroneousness, and most Unchristian and Wicked Spirit of one John Bunyan, Lay-preacher in Bedford." It professes to be written by a friend of Fowler's, but Fowler was generally accredited with it. Its violent tirades against one who, he says, had been "near these twenty years or longer very infamous in the Town and County of Bedford as a very Pestilent Schismatick," and whom he suggests the authorities have done wrong in letting out of prison, and had better clap in gaol again as "an impudent and malicious Firebrand," have long since been consigned to a merciful oblivion, where we may safely leave them.