From some unknown cause, perhaps the depressing effect of protracted confinement, during this second six years Bunyan's pen was far less prolific than during the former period. Only two of his books are dated in these years. The last of these, "A Defence of the Doctrine of Justification by Faith," a reply to a work of Edward Fowler, afterwards Bishop of Gloucester, the rector of Northill, was written in hot haste immediately before his release, and issued from the press contemporaneously with it, the prospect of liberty apparently breathing new life into his wearied soul. When once Bunyan became a free man again, his pen recovered its former copiousness of production, and the works by which he has been immortalized, "The Pilgrim's Progress" - which has been erroneously ascribed to Bunyan's twelve years' imprisonment - and its sequel, "The Holy War," and the "Life and Death of Mr. Badman," and a host of more strictly theological works, followed one another in rapid succession.

Bunyan's second term of imprisonment was certainly less severe than that which preceded it. At its commencement we learn that, like Joseph in Egypt, he found favour in his jailer's eyes, who "took such pity of his rigorous suffering, that he put all care and trust into his hands." Towards the close of his imprisonment its rigour was still further relaxed. The Bedford church book begins its record again in 1688, after an interval of ominous silence of five years, when the persecution was at the hottest. In its earliest entries we find Bunyan's name, which occurs repeatedly up to the date of his final release in 1672. Not one of these notices gives the slightest allusion of his being a prisoner. He is deputed with others to visit and remonstrate with backsliding brethren, and fulfil other commissions on behalf of the congregation, as if he were in the full enjoyment of his liberty. This was in the two years' interval between the expiration of the Conventicle Act, March 2, 1667-8, and the passing of the new Act, styled by Marvell, "the quintessence of arbitrary malice," April 11, 1670. After a few months of hot persecution, when a disgraceful system of espionage was set on foot and the vilest wretches drove a lucrative trade as spies on "meetingers," the severity greatly lessened. Charles II. was already meditating the issuing of a Declaration of Indulgence, and signified his disapprobation of the "forceable courses" in which, "the sad experience of twelve years" showed, there was "very little fruit." One of the first and most notable consequences of this change of policy was Bunyan's release.

Mr. Offor's patient researches in the State Paper Office have proved that the Quakers, than whom no class of sectaries had suffered more severely from the persecuting edicts of the Crown, were mainly instrumental in throwing open the prison doors to those who, like Bunyan, were in bonds for the sake of their religion. Gratitude to John Groves, the Quaker mate of Tattersall's fishing boat, in which Charles had escaped to France after the battle of Worcester, had something, and the untiring advocacy of George Whitehead, the Quaker, had still more, to do with this act of royal clemency. We can readily believe that the good-natured Charles was not sorry to have an opportunity of evidencing his sense of former services rendered at a time of his greatest extremity. But the main cause lay much deeper, and is connected with what Lord Macaulay justly styles "one of the worst acts of one of the worst governments that England has ever seen" - that of the Cabal. Our national honour was at its lowest ebb. Charles had just concluded the profligate Treaty of Dover, by which, in return for the "protection" he sought from the French king, he declared himself a Roman Catholic at heart, and bound himself to take the first opportunity of "changing the present state of religion in England for a better," and restoring the authority of the Pope. The announcement of his conversion Charles found it convenient to postpone. Nor could the other part of his engagement be safely carried into effect at once. It called for secret and cautious preparation. But to pave the way for it, by an unconstitutional exercise of his prerogative he issued a Declaration of Indulgence which suspended all penal laws against "whatever sort of Nonconformists or Recusants." The latter were evidently the real object of the indulgence; the former class were only introduced the better to cloke his infamous design. Toleration, however, was thus at last secured, and the long-oppressed Nonconformists hastened to profit by it. "Ministers returned," writes Mr. J. R. Green, "after years of banishment, to their homes and their flocks. Chapels were re-opened. The gaols were emptied. Men were set free to worship God after their own fashion. John Bunyan left the prison which had for twelve years been his home." More than three thousand licenses to preach were at once issued. One of the earliest of these, dated May 9, 1672, four months before his formal pardon under the Great Seal, was granted to Bunyan, who in the preceding January had been chosen their minister by the little congregation at Bedford, and "giving himself up to serve Christ and His Church in that charge, had received of the elders the right hand of fellowship." The place licensed for the exercise of Bunyan's ministry was a barn standing in an orchard, once forming part of the Castle Moat, which one of the congregation, Josias Roughead, acting for the members of his church, had purchased. The license bears date May 9, 1672. This primitive place of worship, in which Bunyan preached regularly till his death, was pulled down in 1707, when a "three-ridged meeting-house" was erected in its place. This in its turn gave way, in 1849, to the existing more seemly chapel, to which the present Duke of Bedford, in 1876, presented a pair of noble bronze doors bearing scenes, in high relief, from "The Pilgrim's Progress," the work of Mr. Frederick Thrupp. In the vestry are preserved Bunyan's chair, and other relics of the man who has made the name of Bedford famous to the whole civilized world.