Indwelling Sin: Is There Hope?

Read more about indwelling sin in the author's previous post.

Owen, in the opening chapter of his work The Mortification of Sin states that, “The vigor, and power, and comfort of our spiritual life depends on the mortification of the deeds of the flesh.”[1]Owen’s goal for this work, according to Andrew Thompson, was to, “Escape from the region of public debate and to provide something of general use” for the people of his day.[2]

The Mortification of Sin, then, is a deeply practical and useful devotional work rather than an academic and polemical tome. The textual focus of this work is Romans 8:13, “For if you live according to the flesh you will die, but if by the Spirit you put to death the deeds of the body, you will live.” In this verse Owen finds both the necessity and the means of mortification. The necessity of mortification is found in the fact that to continue to live according to the flesh leads to spiritual death. As Owen puts it, “Be killing sin or it will be killing you.”[3]

The means of mortification is found in the fact that it is by the Spirit alone that deeds of the body are put to death. In Owen’s words, “Not to be daily employing the Spirit and new nature for the mortifying of sin, is to neglect that excellent succor which God hath given us against our greatest enemy.”[4] We will deal with these two aspects of mortification in turn. 

The Necessity of Mortification

Owen writes in his chapter on the necessity of mortification, “There is not a day but sin foils or is foiled, prevails or is prevailed on; and it will be so whilst we live in this world.”[5] For the Christian, the necessity of mortification, of killing sin, is founded in the fact that our enemy never sleeps and never grows weary. As Owen goes on, “there is no safety against it but in a constant warfare.”[6] The Christian life is one of this constant warfare, because the battle is always raging in our hearts. As we have already established, this battle is between the law of sin and the law of the Spirit. We do not fight in the hope to win the ultimate victory, but because we know that the ultimate victory has been won by Jesus Christ. 

 Now, what does it mean that sin does not grow weary in its warfare? It means that it does not rest until it has captured our whole heart and led us into the most grievous sin.  As Owen writes, “Sin aims always at the utmost; every time it rises up to tempt or entice, might it have its own course, it would go out to the utmost sin in that kind. Every unclean thought or glance would be adultery if it could; every covetous desire would be oppression, every thought of unbelief would be atheism, might it grow to its head.”[7]

This is the warning to the Christian that is one of the bases of the necessity of mortification: sin will destroy all of us if we do not mortify it by the Spirit. As Owen goes on, “When poor creatures will take blow after blow, wound after wound, foil after foil, and never rouse themselves to a vigorous opposition, can they expect anything but to be hardened through the deceitfulness of sin, and that their souls should bleed to death?”[8] Neglect of mortification is neglect of the soul. For the Christian, the mortification of sin is necessary because sin does not grow weary and will have all of them if it can. 

Mortification is necessary for both negative positive reasons. As we have seen, it is necessary to avoid the negative consequences unmortified sin. But mortification is also necessary to achieve the positive vision that God has set forth for his people in his Word. As Owen writes, “It is our duty to be perfecting holiness in the fear of God, to be growing in grace every day, to be renewing our inward man day by day. Now this cannot be done without the daily mortifying of sin. Sin sets its strength against every act of holiness.”[9]

God has set apart a people for himself by the blood of Christ. Those people, his church, are called to pursue holiness, to grow in grace, and to live lives that are set apart for God. This positive vision for the Christian life, the pursuit of God, is impossible without the identification and mortification of indwelling sin. So even as the Christian pursues mortification to avoid being overtaken and destroyed, the Christian should pursue mortification with the goal of living a life set apart for God, a life of thanksgiving and holiness.

The Means of Mortification  

Rooted in Romans 8:13, Owen contends that the only true means of mortification is the Holy Spirit. He writes, “He only is sufficient for this work; all ways and means without him are as a thing of naught; and he is the great efficient of it, he works in us as he pleases.”[10] This truth is paramount to understanding Owen’s conception of mortification. While it is true to say that mortification is something that we do, it is more accurate to say that mortification is something that is done in us. Mortification is worked in us by the power of the Holy Spirit. 

Owen establishes this point in contrast to a Catholic understanding of mortification. In this, we see the Reformed and Protestant nature of Owen’s theology of indwelling sin. He writes, “The greatest part of popish religion, of that which looks most like religion in their profession, consists in mistaken ways and means of mortification.”[11]

Why is the Catholic understanding of mortification mistaken? According to Owen, “Because those things that appointed of God as means are not used by them in their due place and order – such as are praying fasting, watching, meditation, and the like. These have their use in the business at hand; but whereas they are all to be looked on as streams, they look on them as the fountain.”[12]

For Owen, Catholic mortification is mistaken because it looks at the streams of mortification as the fountain. This is to say that the Holy Spirit does indeed work through secondary means (such as prayer, fasting, and meditation) but these secondary means are never to be understood as the primary means. Prayer, fasting, and meditation are nothing in themselves if not empowered by the Holy Spirit and by faith. 

According to Owen, these duties, done in themselves do nothing but subdue the flesh, leaving sin unharmed. He writes, “Attempting rigid mortification, they fell upon the natural man instead of the corrupt old man, upon the body wherein we live instead of the body of death.”[13] This rigid mortification refers to the ascetic practices common to the monastic movement and broader Catholicism. 

The point that Owen is trying to make with this statement is that ascetic practices, while they can be helpful, will only ever mortify the body if done in themselves. One can train themselves to abstain from sexual pleasure but leave the sin of lust unmortified. One can train themselves to go without food but leave the sin of gluttony unmortified. This leaves the Christian in a tragic state. As Owen writes, 

“Men are galled with the guilt of sin that hath prevailed over them; they instantly promise to themselves and God that they will do so no more; they watch over themselves, and pray for season, until this heat waxes cold, and the sense of sin is worn off; and so mortification goes also, and sin returns to its former dominion. Duties are excellent food for the unhealthy soul; but they are no medicine for a sick soul. He that turns his meat into his medicine must expect no great operation.”[14]

The tragic state of the Christian left to themselves is that none of their duties can avail them mortification. As Owen goes on, “A soul under the power of conviction from the law is pressed to fight against sin, but hath no strength for the combat.”[15] The Christian is totally dependent on the power of the Holy Spirit for the mortification of sin.

Owen gives us two reasons why mortification is the work of the Holy Spirit. 

First, because he is the one who God promised in Ezekiel would be given to us to take away the heart of stone and to give us a heart of flesh.[16] This is the eschatological hope of Scripture, referenced by Owen in Indwelling Sin in Believers, that God would place his law in our hearts and would give us a new heart so that we may worship and obey him rightly. This is the work of the Holy Spirit. 

Second, he writes, “We have all our mortification from the gift of Christ, and all the gifts of Christ are communicated to us and given us by the Spirit of Christ.”[17] This means that our mortification must be from the Holy Spirit because it is he who communicates to us what Christ has won for us. And mortification was won for us by the merits of Christ.[18]

How does the Holy Spirit work mortification in us?

First, he renews us and causes us to abound in grace and the fruits that are contrary to the law of sin. Owen cites Galatians 5:22-24 in support of this. It reads: “But the fruit of the Spirit is love, joy, peace, patience, kindness, goodness, faithfulness, gentleness, self-control; against such things there is no law. And those who belong to Christ Jesus have crucified the flesh with its passions and desires.” The Holy Spirit causes these fruits, which are contrary to the law of sin (the flesh), to abound in our hearts so that that the power of sin is weakened. As Owen explains, “This renewing of us by the Holy Ghost, as it is called, is one great way of mortification; he causes us to grow, thrive, flourish, and abound in those graces which are contrary, opposite, and destructive to all the fruits of the flesh.”[19]

Second, the Holy Spirit drives our lusts and sins out of our heart. As Owen points out, in Isaiah 4:4 he is called a Spirit of judgement and burning which “washed away the filth of the daughters of Zion and cleansed the bloodstains of Jerusalem”.[20]

Finally, the Holy Spirit, according to Owen, “Brings the cross of Christ into the heart of a sinner by faith, and gives us communion with Christ in his death and fellowship in his sufferings.”[21]

Owen makes a point here that is essential to understanding his conception of the Gospel, the Trinity, and the order of salvation. For Owen, and many other Protestant reformers, the Holy Spirit is the person of the Trinity who applies to the heart of the believer the accomplishments of Christ.

In Christ we are justified and made righteous by his perfect life, innocent death, and resurrection. By the Spirit we are born again, given the gifts of faith and repentance, and given the seal of God’s presence in our hearts. This understanding of the Father as the author of our salvation, the Son as the accomplisher of our salvation, and the Holy Spirit as the one who applies our salvation is one of key truths which springs from Sola Gratia and Sola Christus Reformation theology. 

So, if the question is: is the mortification of each and every sin possible? The answer, Scripturally, is a deep and resounding yes! And the answer is yes because of the Spirit of Christ.

One might ask: why we are commanded in Romans 8:13 to mortify our sin if it is the Holy Spirit who does this work in us? Owen’s answer to this question is rooted in Philippians 2:12-13, in which Paul instructs us to, “Work out your own salvation with fear and trembling, for it is God who works in you, both to will and to work for his good pleasure.” 

The Holy Spirit, according to Owen, “Works in us and upon us…so as to preserve our own liberty and free obedience…he works in us and with us, not against us or without us; so that his assistance is an encouragement as to the facilitating of the work, and no occasion of neglect as to the work itself.”[22] So, even as we work at mortification, in obedience and faith, God by his Spirit is working, helping, and empowering our every energy and effort.

There are several activities that aid in the mortification of sin that Owen reviews in his work: 

  • First, the Christian should consider and meditate deeply on both the holiness of God and the wickedness of their own sin. Owen explains, “Be much in thoughtfulness of the excellency of the majesty of God and thine infinite, inconceivable distance from him. Many thoughts of it cannot but fill thee with a sense of thine own vileness, which strikes deep at the root of any indwelling sin.”[23] This activity is one that should bring the Christian into a state of humility, of dependence on God, and of hatred for their indwelling sin. It is only when we are made low and our sin is hated as our enemy that we are open to receive the Gospel work of Spirit-wrought mortification.
  • Second, the Christian should set their faith in Christ and his merits for the mortification of their sin. Owen explains, “Set faith at work on Christ for the killing of thy sin. His blood is the great sovereign remedy for sin-sick souls. Live in this, and thou wilt die a conqueror; yes, thou wilt, through the good providence of God, live to see thy lust dead at thy feet.”[24] This act of faith brings us into a position of dependence on Christ and calls us to consider all the provision for mortification given to us in Christ. In faith, as Owen writes, the Christian should, “Raise up thy heart by faith to an expectation of relief from Christ.”[25] This position of humility, faith, and dependence is the ground on which the Holy Spirit pours his life-giving water. Through these Spirit-empowered activities, by prayer and petition, the mortification of indwelling sin is worked.

Daniel B. Miller serves as the Assistant Pastor at First Church, PCA in Lansing, IL.

Related Links

"The Pure Pursuit" by Ben Franks

"Sanctification: The Definitive Aspect" by David Smith

"Keep Advancing!" by Joel Wood

"The Gospel for Bruised Reeds" by Dan Doriani

Growing in Grace, ed. by Joel Beeke

Sanctification: The Long Journey Home, with Derek Thomas and Greg Gilbert


Owen, John. Indwelling Sin in Believers. Reprint edition. Edinburgh: Banner of Truth, 2010.

______. The Mortification of Sin. CreateSpace Independent Publishing Platform, 2012.

Thomson, Andrew. John Owen: Prince of Puritans. Christian Focus Publications, 2016.


[1] John Owen, The Mortification of Sin (CreateSpace Independent Publishing Platform, 2012), 13 

[2] Thomson, John Owen, 79. 

[3] Owen, The Mortification of Sin, 14.

[4] Ibid., 18.

[5] Ibid., 17.

[6] Ibid.

[7] Ibid.

[8] Ibid.

[9] Ibid.

[10] Ibid., 23.

[11] Ibid., 24.

[12] Ibid.

[13] Ibid., 25.

[14] Ibid.

[15] Ibid., 28.

[16] Ibid. See also Ezekiel 11:19, 36:26.

[17] Ibid., 26.

[18] Acts 5:31.

[19] Owen, The Mortification of Sin, 27.

[20] Ibid.

[21] Ibid.

[22] Ibid., 28.

[23] Ibid., 87.

[24] Ibid., 107.

[25] Ibid., 108.