Devotional 68: The Work of Sanctification: Being Transformed by the Spirit

The Confession Read

They who are effectually called and regenerated, having a new heart and a new spirit created in them, are further sanctified, really and personally, through the virtue of Christ's death and resurrection, by His Word and Spirit dwelling in them: the dominion of the whole body of sin is destroyed, and the several lusts thereof are more and more weakened and mortified; and they more and more quickened and strengthened in all saving graces, to the practice of true holiness, without which no man shall see the Lord.

— Westminster Confession of Faith, Chapter 13, Section 1

Introduction

He had been a believer for seven years when the discovery came, not as a thunderclap but as the slow dawning of a truth he had never been taught to expect. He had imagined, as many young converts do, that conversion was the end of the war. The old man was dead, buried with Christ in baptism; the new man had risen to walk in newness of life. Surely, he reasoned, the impulses that once mastered him, the sudden flares of temper, the undertow of lust, the cold currents of envy, would wither now, starved of the consent they once commanded. And indeed, some things had passed away. The coarse language that once rolled easily from his tongue now felt foreign. The appetites that had ruled his evenings had lost their commanding voice. He was not what he had been. And yet the old man was not so dead as he had supposed. A word spoken against him still kindled a flash of wounded pride before grace could extinguish it. A season of prosperity still bred a subtle self-reliance that prayer only haltingly corrected. He was changed, deeply and truly. But he was not finished. The war had not ended at conversion; it had only begun in earnest. The enemy that once possessed the citadel had been driven from the throne room, but he still held outposts in the outer provinces, and he contested every inch of ground. This experience, common to every believer who has walked with Christ long enough to know his own heart, is the territory into which the thirteenth chapter of our Confession steps. The chapter is titled "Of Sanctification," and though it runs only three sections, its first section, which we take up now, holds pastoral wisdom that has steadied many pilgrims. It answers the practical questions the Christian life poses: If I am truly born again, why do I still struggle with sin? What has actually happened to sin's power over me? And how does the Holy Spirit carry forward the work that Christ has begun? The Divines place sanctification here, after calling, justification, and adoption, in the unfolding chain of salvation. The order is not arbitrary. Those who are effectually called and regenerated, brought from death to life by the sovereign voice of the Son of God and given a new heart, are the subjects of this further work. Sanctification does not make a man a Christian; it takes the man who is already a Christian and makes him more like Christ. It is the fruit of grace, not its root — the superstructure that grows upon the foundation. And yet the Confession insists, with the weight of all Scripture behind it, that there is no salvation without it, for "without holiness no man shall see the Lord."

Scripture Foundation

The Apostle Paul opens the sixth chapter of Romans with a question that arises inevitably from the doctrine he has just expounded. If grace abounds where sin abounds, if justification is by faith apart from works, then what restraint remains upon the justified sinner? Shall we continue in sin that grace may abound? The answer is a horrified negative: mē genoito, "God forbid," the strongest negation the Greek language can supply, followed by a concentrated exposition of sanctification in Scripture. In Romans 6:1-14 Paul writes: "How shall we, that are dead to sin, live any longer therein? Know ye not, that so many of us as were baptized into Jesus Christ were baptized into his death? Therefore we are buried with him by baptism into death: that like as Christ was raised up from the dead by the glory of the Father, even so we also should walk in newness of life." Every clause aligns with a phrase in the Confession. "Our old man is crucified with him" — the decisive break with sin's reign. "That the body of sin might be destroyed" — the Greek katargēthē, rendered "destroyed" in the Authorized Version, means to render inoperative, to strip of power, to dethrone. It does not mean to annihilate. Sin remains, but it no longer reigns. The tyrant has been deposed, though pockets of resistance remain. But Paul does not stop with the negative. He moves to the positive: "Likewise reckon ye also yourselves to be dead indeed unto sin, but alive unto God through Jesus Christ our Lord." The verb logizesthe, "reckon," is accounting language: count it as true because it is true. And then the imperative: "Let not sin therefore reign in your mortal body." The reign is broken, but the believer must enforce the victory. The dethroned king still issues commands; the believer must refuse to obey. This is the paradox of sanctification, and the Confession captures both sides: the dominion is destroyed, yet the lusts must be progressively mortified. Turn to the Apostle's second letter to the Corinthians, where the progressive character of sanctification is expressed in striking language. In 2 Corinthians 3:18 Paul writes: "But we all, with open face beholding as in a glass the glory of the Lord, are changed into the same image from glory to glory, even as by the Spirit of the Lord." The verb "are changed," metamorphoumetha, from which we derive "metamorphosis", is present passive: we are being transformed, continuously, by an agency outside ourselves. The transformation is into the likeness of Christ, "the same image," and it proceeds "from glory to glory," by successive degrees. The instrument? "Beholding as in a glass the glory of the Lord." The Greek katoptrizomenoi suggests looking into a mirror, and the mirror is the gospel — the Word of God in which Christ's glory is displayed. As the believer gazes upon Christ in the Scriptures, the Spirit uses that very beholding to conform the beholder to what he sees. The Word presents Christ; the Spirit transforms the soul into His likeness; the two means are inseparably joined — precisely the Confession's teaching that sanctification is wrought "by His Word and Spirit dwelling in them." The Apostle to the Galatians draws the battle lines with the sharpness of a veteran who has seen the carnage of spiritual war. In Galatians 5:16-17, 24-25 he writes: "This I say then, Walk in the Spirit, and ye shall not fulfil the lust of the flesh. For the flesh lusteth against the Spirit, and the Spirit against the flesh: and these are contrary the one to the other: so that ye cannot do the things that ye would." The verb "walk," peripateite, is a present imperative, calling for a continuous manner of life in conscious dependence upon the indwelling Spirit. The promise is absolute: "ye shall not fulfil the lust of the flesh." The Greek epithumia points to the flesh as a unified principle of rebellion: the "whole body of sin" of the Confession. The Spirit and the flesh are at war; the Greek strateuetai suggests a military campaign, and the result is that the believer "cannot do the things that ye would." Here is the frustration of the sanctified soul: the new nature desires holiness, but the remaining flesh resists, so that even the believer's best obedience is mixed with failure. Then the decisive declaration: "And they that are Christ's have crucified the flesh with the affections and lusts." The verb estaurōsan is aorist: a definitive act accomplished in the past. At conversion, the believer crucified the flesh, not by his own power but by participation in Christ's crucifixion. Yet the very next verse implies that this crucifixion is not the end of responsibility: "If we live in the Spirit, let us also walk in the Spirit." The indicative grounds the imperative; the accomplished fact calls for the continuing response. This is the two-sidedness the Confession captures: dominion destroyed, yet lusts progressively weakened. One further passage brings the human and the divine into their proper relation. In Philippians 2:12-13 Paul writes: "Work out your own salvation with fear and trembling. For it is God which worketh in you both to will and to do of his good pleasure." "Work out," katergazesthe, is not "work for"; Paul never tells the believer to earn his salvation. The verb means to bring to completion, to carry through to the end what God has already worked in. "With fear and trembling" is not servile dread but the reverent awe of a creature who knows the Almighty is at work within him. The ground of this solemn diligence is the declaration that follows: "For it is God which worketh in you." The Greek energōn is a present participle: God is continually, actively, energetically at work, producing both the desire for holiness and the execution of it. The believer works because God works. Grace does not make the believer passive; grace makes the believer active, for the grace that saves is also the grace that empowers. Finally, the Confession closes with a phrase that falls like a hammer on every form of antinomian complacency: "without which no man shall see the Lord." The text is drawn from Hebrews 12:14: "Follow peace with all men, and holiness, without which no man shall see the Lord." The Greek hagiasmon, holiness or sanctification, is an objective reality, not a subjective feeling. The verb "follow," diōkete, means to pursue, to chase down with relentless determination. Holiness is not a state into which the believer drifts; it is a prize for which he strives. The vision of God Himself, the beatific vision that is the final hope of every redeemed soul, is contingent upon holiness. Not because holiness merits the vision, but because holiness is the necessary preparation for it. A sinful creature cannot see a holy God and live, and therefore the God who intends His people for the vision of His face prepares them by making them holy. Sanctification is the road to glory, and there is no other road.

What the Divines Meant

When the Westminster Assembly convened in the Jerusalem Chamber, the doctrine of sanctification was not the most contentious item on the docket. The great battles of the Reformation had been fought over justification, and the Council of Trent had anathematized the Reformed doctrine. The Assembly had already, in Chapter 11, set forth justification with uncompromising clarity. But the Divines understood that a right doctrine of justification, if not balanced by an equally right doctrine of sanctification, could be twisted into opposite and equally deadly errors. On one side stood the Antinomians, who argued that since believers are justified by grace through faith apart from works, the moral law has no claim upon them. Sin in the believer, they taught, is not truly sin, or if it is sin it is already forgiven and need not trouble the conscience. This error was not a straw man; it had flesh-and-blood advocates in England during the 1640s, and its fruits were visible in congregations where professions of faith multiplied while holiness of life decayed. The Divines confronted this not by qualifying justification but by expounding sanctification. Yes, justification is by faith alone. But the faith that justifies is never alone; it is always accompanied by the Spirit who sanctifies. If a man claims to be justified while living contentedly under sin's dominion, his claim is false. The gospel that does not produce holiness is not the gospel. On the other side stood perfectionist teachings: from the Anabaptist wing, from medieval mysticism, and from the new "enthusiasm" of the Quakers. These groups taught, in various forms, that the believer could attain sinless perfection in this life, either at a single crisis moment subsequent to conversion or through the inward light progressively eradicating the old nature. Against this, the Divines insisted on the gradual character of sanctification: "more and more weakened and mortified," "more and more quickened and strengthened." The progressive tenses are deliberate. Sanctification is a gradual process, not a single crisis — a long campaign rather than one decisive moment. And the campaign lasts until death. The opening clause establishes that sanctification presupposes effectual calling and regeneration. The Divines carefully distinguished the Spirit's various works. Regeneration is the instantaneous impartation of spiritual life to the dead soul, the creation of a new heart and a new spirit. Sanctification is the subsequent, progressive work by which that new life is exercised and brought to maturity. The new heart is the soil; sanctification is the cultivation. The one who has not been regenerated cannot be sanctified, for there is no new nature to cultivate. But the one who has been regenerated will be sanctified, for the Spirit who planted the new nature will not abandon it. The phrase "really and personally" was aimed at those who reduced sanctification to a change in legal status. In justification, the believer's standing changes: he is declared righteous. In adoption, his relation changes: he is declared a son. But in sanctification, something more radical happens: he himself changes. The change is "real": not a legal fiction but an actual transformation. And the change is "personal": not an abstract alteration but a renovation of the whole man: understanding, will, affections, conscience, memory, body. The source of this transformation is "the virtue of Christ's death and resurrection." The word "virtue" carries its older Latin sense of virtus: power, efficacy, strength. Sanctification does not flow from a second, separate work of Christ but from the same death and resurrection that purchased justification. The believer, united to Christ in His death, finds that sin's power is progressively put to death. United to Christ in His resurrection, he finds that graces are progressively brought to life. The same power that raised Jesus from the dead is at work in the believer, not to raise his body on the last day alone, but to raise his soul from the death of sin in the present day. The means are two: "His Word and Spirit dwelling in them." These are not alternative routes but conjoined instruments. The Spirit does not ordinarily work apart from the Word, leading by inward impulses disconnected from Scripture. Nor does the Word work apart from the Spirit, as though the bare letter could transform the soul. The Spirit speaks through the Word; the Word is the sword of the Spirit. When the believer reads Scripture with a heart opened by the Spirit, commands direct his obedience, promises sustain his hope, warnings restrain his sin, and above all, the revelation of Christ draws his affections heavenward. This is why the man who neglects his Bible stagnates in sanctification, however earnestly he may pray. The Spirit has bound Himself to His own Word, and He will not honor a pretended dependence that disdains the appointed means. Then comes the twofold description of what sanctification accomplishes. On the negative side: "the dominion of the whole body of sin is destroyed." The "body of sin" is Paul's phrase from Romans 6:6: the organized mass of sinful inclinations, habits, and dispositions that constitutes the old man. Its dominion, its ruling power, is broken at conversion. The believer may still sin, but he does not sin with the whole-hearted consent of his nature. There is a new principle within that resists, grieves, and protests. The tyrant still shouts commands; the citizen no longer obeys them as his lawful sovereign. Yet the destruction of dominion is not the annihilation of the enemy. The "several lusts" are "more and more weakened and mortified." The Greek verb nekrōsate in Colossians 3:5 means to put to death. The believer is engaged in a lifelong work of execution: identifying remaining lusts, tracking them to their lairs, putting them to death by the Spirit's power. Progress is real but gradual, and never complete in this life. The Confession's "more and more" is sober realism that distinguishes Reformed piety from every form of triumphalism. On the positive side: believers are "more and more quickened and strengthened in all saving graces." "Quickened," from the Latin vivificare, means made alive. Sanctification is not merely the removal of sin but the cultivation of righteousness. Faith is strengthened, love deepened, hope brightened, patience lengthened, humility heightened. Every grace implanted at regeneration is progressively exercised and confirmed. The result is "the practice of true holiness": not a holiness that exists only in profession but one that becomes visible in daily life. The closing quotation from Hebrews 12:14 — "without which no man shall see the Lord" — is a severe warning, yet it is also, rightly understood, a real comfort. It tells the believer that his struggle for holiness is not a sideshow but the main road. Every battle with besetting sin, every prayer for strength, every tear of repentance after a fall, every small victory over entrenched habit — these are the Spirit's work of preparing the believer for the vision of God. The command is absolute, but the power is supplied. The end is certain: those whom God has called and justified He will also sanctify, and having sanctified them, He will bring them at last to see His face.

Theological Depth

John Owen devoted the concentrated energies of his mature ministry to the doctrine of sanctification, and his little volume Of the Mortification of Sin in Believers remains, after more than three centuries, the most searching practical treatise on the subject in English. Owen understood that the great pastoral question is not whether believers must fight sin but how. His famous dictum, "Be killing sin or it will be killing you," is not a threat but a diagnosis. The sin that the believer tolerates or neglects will not remain static; it will grow. Sin is always either advancing or retreating. Owen grounded mortification upon the very truth this section of the Confession articulates: the dominion of sin is broken, but its presence remains. His counsel was intensely practical. The believer must know his own heart well enough to identify his particular besetting sins, for the enemy attacks not with a general offensive but at the points of greatest weakness. He must load his conscience with the guilt of those sins — not to drive himself to despair, but to fuel the hatred without which mortification is half-hearted. He must bring the cross of Christ to bear upon each lust, for sin is only put to death by the power of Christ's death. And he must do all this in reliance upon the Spirit, for mortification is not a technique but a grace. Owen's teaching, for all its rigor, breathes the atmosphere of Romans 8: there is no condemnation for those who are in Christ Jesus, and the Spirit who indwells them is the Spirit of life. John Murray contributed a refinement that has shaped Reformed understanding. In his essay "Definitive Sanctification," Murray argued that the New Testament speaks of sanctification in two distinct senses. There is the definitive, once-for-all sanctification at conversion: the believer is "sanctified in Christ Jesus" (1 Corinthians 1:2), "sanctified by the offering of the body of Jesus Christ once for all" (Hebrews 10:10). This is the breaking of sin's dominion, the decisive separation from its reigning power. And then there is progressive sanctification: the believer is "being sanctified" (Hebrews 10:14, present participle), growing in holiness by degrees. Murray insisted that the definitive must ground the progressive. The believer does not fight for victory but from victory. The dominion is broken; the battle that remains is the mopping-up operation against an already-defeated enemy. This insight, latent in the Confession's distinction between destruction of dominion and progressive weakening of lusts, has proved a pastoral balm for believers who mistake the ongoing presence of sin for the absence of any real change. Calvin, who treated sanctification under the broader heading of regeneration in the Institutes, always insisted that the grace of Christ is a twofold gift. In union with Christ, the believer receives both justification and sanctification, inseparable though distinct. Calvin's great contribution was to root sanctification in union with Christ rather than in the believer's own moral effort. "We are justified," he wrote, "not without works, yet not by works, since in the participation of Christ, by which we are justified, sanctification is contained just as much as righteousness." The believer's growth in holiness is not the cause of his acceptance with God but the necessary outflow of his union with the One who is his righteousness. Where union with Christ is, sanctification will follow, for Christ does not give Himself partially. Every advance in holiness is the gift of the indwelling Christ through the indwelling Spirit. Thomas Watson, expounding sanctification in his Body of Divinity, observed that it is the only infallible evidence of justification. A man may profess faith, enjoy religious experiences, perform religious duties, and yet remain unsanctified. But where the Spirit has begun the work of making a man holy, there is a signature that cannot be counterfeited. Watson urged self-examination: Does sin grieve you? Does remaining corruption burden your conscience? Do you find within a holy principle that wars against the flesh? These are the marks of the sanctified soul, and they are far more reliable than the memory of a conversion experience or the fluency of a testimony. Yet Watson was equally concerned to comfort the true believer who reads this section and despairs. If sanctification means progressive weakening of sin, and I seem to be making no progress — indeed, if I seem more aware of my sin now than when I first believed — am I truly sanctified? Watson answered with the wisdom of a physician who knows the difference between symptoms and signs of cure. The man who is most sanctified feels his remaining corruption most keenly, because his spiritual senses have been sharpened. The very grief you feel over your lack of progress is evidence the Spirit has not abandoned you. A dead man feels no pain; a living man feels the surgeon's knife. Let the pain of remaining sin drive you to Christ, not from Him.

Puritan Application

First, distinguish carefully between the decisive and the progressive. The Confession sets before you a twofold truth that, held in balance, will steady your Christian walk through every season. On the one hand, the dominion of sin is destroyed — the decisive, irreversible accomplishment of your union with Christ in His death and resurrection. If you are in Christ, sin is no longer your master. It may shout, threaten, and bribe, but it cannot command your obedience with the authority it once possessed. On the other hand, sin's presence remains, and its individual lusts are being progressively weakened and mortified. The believer who forgets the first truth sinks into despair, imagining that the continuing strength of temptation proves he was never truly converted. The believer who forgets the second truth grows complacent, imagining that because the dominion is broken, the battle is over. Hold both with equal firmness: you are free, and you must fight. The freedom grounds the fighting, and the fighting proves the freedom. Second, make the Word the daily instrument of your sanctification. The Spirit who dwells in you has bound Himself to the Scriptures as His chosen tool. He will not ordinarily sanctify you apart from the Word, any more than a farmer expects a harvest without seed. Read the Scriptures as the appointed means by which the Spirit renews your mind, not as a duty to be discharged. Approach them systematically, so the whole counsel of God shapes your understanding; meditatively, pausing until truth penetrates the heart rather than only the intellect; and prayerfully, asking the Spirit who inspired them to illuminate and apply them. Keep a particular eye on Christ as you read, for the glory of Christ is the transformative power of the Word. As you behold Him there, His holiness, His humility, His patience, the Spirit uses that beholding to conform you to what you see. The man who neglects his Bible yet prays for holiness is like a man who refuses food yet prays for strength. God has appointed the means; use them, and trust Him to bless them. Third, do not mistake the pain of sanctification for the absence of grace. The old divines spoke of mortification as a bloody work, and they were not exaggerating. To put sin to death is to cut off what has been dear to you: to pluck out the right eye, to crucify the flesh with its affections and lusts. This is not pleasant. The man who expected conversion to be the end of all struggle discovers, often with dismay, that the struggle has only intensified, for now a new nature resists the old, and the collision of the two is painful. Do not conclude from the intensity of the conflict that you are losing. The very fact that you are fighting — that sin grieves you, that you resist it, that you return to the cross again and again for pardon and power — is evidence the Spirit is at work within you. The man who has ceased to struggle has ceased to be sanctified. The question is not whether you fight, but on whose strength you rely. Look to Christ. His death is the death of your sin; His resurrection is the life of your holiness. The battle belongs to the Lord, and the Lord is on your side. Fourth, pursue holiness as the necessary evidence of your salvation, but never as the ground of it. The Confession closes with the most searching words in the entire section: "without which no man shall see the Lord." This is not a threat to make you doubt your salvation but a goad to keep you from presuming upon it. Holiness is the path to glory, and there is no other path. Examine yourself with honesty. Is there a war within you against sin? Do you hate the sin that you still commit? Is your life, in its overall trajectory, moving toward Christlikeness? These are the marks of the sanctified soul, and where they are absent, there is reason for urgent alarm. But where they are present — even when weak, intermittent, and mixed with much failure — there is reason for hope. Your hope is not that your holiness is sufficient, but that the Spirit who began the work will complete it. He who called you is faithful; He will also do it. Pursue holiness with all the energy that grace supplies, but rest your soul's weight not on your pursuit but on Christ's righteousness. Fifth, learn to see your trials as your Father's instruments of sanctification. The Confession does not here directly address the role of suffering in sanctification; that belongs to the chapter on providence, but the principle is implicit throughout. The Spirit who sanctifies uses every circumstance of life as His workshop. The disappointment that shatters your plans is the Spirit weaning you from self-reliance. The difficult person whose presence grates upon your patience is the Spirit's appointed instrument for cultivating the forbearance of Christ. The season of spiritual dryness, when the heavens seem brass and your prayers bounce back from the ceiling, is not evidence that God has abandoned you; it is the Spirit teaching you to walk by faith and not by sight, to cling to the promise when the feeling is withdrawn. The believer who learns to interpret his circumstances through the lens of sanctification finds meaning even in the most bewildering providences. Every tear and trial, every thorn in the flesh, is being woven by the Spirit into the fabric of your holiness. The day will come when you will thank God for the very afflictions you now beg Him to remove, for you will see that they were the tools by which He carved the image of His Son into your soul.

Prayer

O Lord our God, who hast called us out of darkness into thy marvellous light, who hast justified us freely by thy grace through the redemption that is in Christ Jesus, and who hast adopted us as thy children and made us heirs of everlasting salvation: we bless thee that thou dost not leave us as thou didst find us. Thou hast begun a good work in us, a work of real and personal transformation, a work by which the defaced image of God is being restored in our souls. We thank thee that the dominion of sin is broken, that we are no longer the helpless captives of our corruptions, that the tyrant who once reigned unchallenged has been dethroned by the power of Christ's death and resurrection. And yet, O Father, we confess with shame that we do not always live as those who have been set free. The lusts that remain still exert their pull; the habits that grace has weakened still muster their resistance. We have yielded to temptations we should have resisted, neglected duties we should have performed, spoken words we should have left unspoken, and left unsaid the words of kindness and witness we should have spoken. Our sanctification is real, but it is slow, and we are impatient with its slowness and grieved by its imperfection. Forgive us, we pray, and let not our failures become occasions for despair. Let them rather drive us afresh to the cross, where our pardon was purchased, and to the throne of grace, where our help is found. Grant us the Spirit of mortification. Teach us to put to death the deeds of the body, to crucify the flesh with its affections and lusts, to make no provision for sin but to wage unceasing war against every impulse that rises against thy holiness. And grant us also the Spirit of vivification. Quicken us in every saving grace: deepen our faith until it rests with unshakeable confidence upon thy promises; enlarge our love until it embraces not only those who love us but those who oppose us; strengthen our hope until it pierces through the gloom of the present age and fixes upon the glory that is to come. Use thy Word as the daily instrument of our renewal. Open our eyes to behold wondrous things out of thy law. Let the Scriptures be not a duty we discharge but a feast at which we are nourished, a mirror in which we see our sin and our Saviour, a fire that warms our cold hearts and a hammer that breaks our hard ones. And let the Spirit who indited the Word be the Spirit who illuminates and applies it to our hearts. Sanctify our afflictions, O Lord. When thy hand lies heavy upon us, when the way is dark and the burden is heavy, grant that we may not waste our sorrows but find in them the discipline of sons. Let every trial drive us nearer to thee; let every disappointment wean us from the world; let every glimpse of our own weakness teach us to lean more wholly upon thy strength. We would not choose the easy path if the hard path leads to holiness. Bring to completion the work thou hast begun. Hasten the day when faith shall be sight, when the warfare shall be ended and the victory complete. Until that day, keep us fighting the good fight, looking unto Jesus, the author and finisher of our faith, who for the joy that was set before him endured the cross and is set down at the right hand of the throne of God. In his name we pray, who ever liveth to make intercession for us. Amen.