You bet he did! Like most Christians throughout the history of the church, this famous believer was prone to discouragement. When he saw the sway that sin still held in his life he would begin to question whether or not God was really working in him–whether God would indeed keep him.
So what did he do?
Bunyan did excellently what we are so frequently admonishing each other to do: Preach truth to your own heart. A wonderful illustration of this is below.
Here, when faced with fits of despair and discouragement, Bunyan takes the truth of justification (forgiveness of sins and the imputation of Christ’s righteousness) and preaches it to his heart. Despite what he feels, he says to himself, ‘This is what is true. This is where I can find hope, comfort, and peace.’
We would all do well to learn from his example and follow in his footsteps when we are discouraged or downcast.
Sometimes I bless the Lord my soul hath had the life that now I am speaking of, not only imputed to me, but the very glory of it upon my soul; for, upon a time, when I was under many condemnings of heart, and feared, because of my sins, my soul would miss of eternal glory, methought I felt in my soul such a secret motion of this—Thy righteousness is in Heaven, together with the splendour and shining of the Spirit of Grace in my soul, which gave me to see clearly that my righteousness by which I should be justified from all that could condemn, was the Son of God Himself in His own Person, now at the right hand of His Father representing me complete before the Mercy- seat in His Ownself; so that I saw clearly that night and day, wherever I was, or whatever I was a doing, still there was my righteousness just before the eyes of Divine glory; so that the Father could never find fault with me for any insufficiency that was in my righteousness, seeing it was complete; neither could He say, Where is it? because it was continually at His right hand.
Also, at another time, having contracted guilt upon my soul, and having some distemper of body upon me, I supposed that death might now so seize upon as to take me away from among men; then, thought I, what shall I do now? is all right with my soul? Have I the right work of God on my soul? Answering myself, “No, surely”; and that because there were so many weaknesses in me; yes, so many weaknesses in my best duties. For, thought I, how can such an one as I find mercy, whose heart is so ready to evil, and so backward to that which is good, so far as it is natural. Thus musing, being filled with fear to die, these words come in upon my soul, “Being justified freely by His grace through the redemption that is in Christ Jesus” (Rom 3:24). As if God had said, Sinner, thou thinkest because that thou hast had so many infirmities and weaknesses in thy soul while thou hast been professing of Me, therefore now there can be no hopes of mercy; but be it known unto thee, that it was not anything done by thee at the first that moved Me to have mercy upon thee: neither is it anything that is done by thee now that shall make me either accept or reject thee.