Of the Mortification of Sin–Chapter 3–THERE’S HELP!

It’s time to talk about Chapter Three of John Owen’s book, Overcoming Sin and Temptation.

I’ve been reading and discussing one chapter a week of this insightful classic, published in 1656, with an informal group of blog readers.  Every Thursday we converge on the “Comments” section at Challies.com to share our thoughts.  Meanwhile, week by week I’m processing what I read here in loose paraphrase to be sure I ‘get it’.  [I’ve tucked in my own thoughts throughout and added some thoughts of personal application at the end.]  Care to join me for a walk through?



The Holy Spirit is God’s Provision for the mortification of indwelling sin

 Last week Owen made the case for how necessary it is for individual believers to be about the business of mortifying sin daily!  He made his point well: “be killing sin or it will be killing you!”  But how is one to go about that?  This week he clarifies that this work is not to be undertaken single-handedly with any strategy we can concoct.  It is the work of the Spirit of God to accomplish this in us. This is good news.  Why then do we try so hard on our own? Here’s what Owen has to say…


The Holy Spirit is the only one able to accomplish this work.  To attempt it any other way is ‘ruin, damnation, destruction.’  The Spirit ‘works in us as he pleases.’

People have come up with various man-made means of mortification. The Catholic church is cited for example, as being characterized by ‘mistaken ways and means of mortification’ including: the use of rough garments, vows, penance, disciplines, and monastical life.  Owen says they are ‘laboring to mortify dead creatures’ and promises to comment more on this later.

But he says, this is not only true of Catholicism.  Protestants too have adopted similar formulas for mortification.  He calls these ‘self-vexations’.  They include legalistic duties, bodily exercises and other efforts without reference to the Holy Spirit.  Proponents of these means are unacquainted with ‘the power of God and mystery of the gospel’, which is one of the reasons Owen writes this book.

 The reason these methods of mortification fail is that they are not God’s appointed ways.

“In vain do you worship me, teaching for doctrines the traditions of men.” Mt.15:9

God has appointed things like prayer, fasting, watching, and meditation to assist us in mortifying the flesh.  But even these are not to be seen as sources of mortification in themselves.  They must be accompanied by faith and directed by the Spirit if they are to have any effect in mortifying the flesh.  They are not virtues in and of themselves which can be practiced to guarantee mortification.  They may affect the body (the natural man) but will not “mortify lust or corruption”, Owen says.  This is the primary mistake people make who don’t understand the Gospel. This error lies at the root of ‘very much of that superstition and will-worship that has been brought into the world’.

 [I’m intrigued by his term ‘will-worship’ as I tend to put a lot of stock in ‘will power’.  But ultimately, if the case he’s making is correct, no amount of will-power can substitute for the working of the Holy Spirit.  In fact, what I value as will-power, could well be just the flesh, trying to put the flesh to death.  I heard someone say once that it’s impossible to crucify oneself. It takes more hands than we’ve got!]

In Owen’s words: “…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”  

[Now that’s an interesting and often overlooked distinction Our human bodies are not synonymous with ‘the body of death’,–that indwelling propensity to sin.  We can do things that will weaken the physical body without having any weakening effect on the sin that dwells within those bodies.  I am reminded of Colossians 2 where Paul cites certain traditions and taboos prevalent in his day and goes on to say that though they ‘have indeed an appearance of wisdom in promoting self-made religion and asceticism and severity to the body…they are of no value in stopping the indulgence of the flesh.“]


Having decried these attempts at self-mortification, Owen acknowledges that this inclination to ‘will worship’ is a common and  natural inclination.

Here’s how it goes:

You feel guilty for a sin you’ve committed.

You promise yourself and God that you will do better and stop sinning that way.

You’re careful.  You watch yourself. You pray lots, for awhile;  then the urgency of it wears off. 

Mortification also ceases.  The sin returns to dominate you.

Owen then goes on to explain that though certain duties have their place in our spiritual growth, just as food does for our bodies, yet duties will not heal our souls.  Our souls are sick and need more than ‘doing’ to get better.  “Spiritually sick men cannot sweat out their distemper with working.”

The thing that needs to be accomplished in us is far too complex for self-effort to accomplish.  An “almighty energy is necessary.” He promises to comment more on this later.  Having explained the reality that the Spirit is God’s appointed means for our mortification, Owen goes on to explain why and how this is so:

 WHY Mortification Is A Work Of The Spirit

  • God has promised Him to us to do this work.  “I will give my Spirit, and take away the stony heart” (Ezek.11:19)

[I have always just associated this verse with actual regeneration (our salvation) so this is an interesting application.]

  •  The Spirit is Christ’s means of working in the believer’s life.  “Without Christ we can do nothing.” Jn.15:5
  • Christ was exalted for this very purpose, in order to send the Holy Spirit to indwell his followers (see: Acts 5:31 and Acts 2:33), in order “to perform the work on His behalf” (transl. from Latin)


HOW the Spirit mortifies Sin

  • The Spirit renews us as described in Titus 3:5: “the washing of regeneration and renewal of the Holy Spirit” and produces the ‘fruits of the Spirit’ in us.  These fruits are in natural opposition to the flesh and when they abound the sins of the flesh cannot.  As we live by the Spirit and walk after the Spirit sin will be naturally mortified. “If we live by the Spirit, let us also walk by the Spirit” Gal.5:25

 “[The Spirit] causes us to grow, thrive, flourish, and abound in those graces which are contrary, opposite, and destructive to all the fruits of the flesh, and to the quiet or thriving of indwelling sin itself.”  

(I found this thought interesting.  It’s saying that one or the other will thrive in us, either the fruit of the spirit or the fruit of the flesh. We are either sowing to the flesh or to the Spirit, yielding to the flesh or to the Spirit, living by faith and dependence on God or relying on our flesh/selves. There is not some neutral middle ground as we like to think)


  • The Spirit literally changes our hearts. He is called a ‘spirit of judgment  and…burning’ Is.4:4  He weakens, destroys and takes away the root and habits of sin, consuming and destroying our lusts.  This taking away of our stony hearts is a supernatural act of Almighty God in us begun at conversion and continued in our sanctifying process.


  • The Spirit brings the cross of Christ to bear on our sinful hearts by faith, giving us ‘communion with Christ in his death and fellowship in his sufferings.’ Owen promises to explain this later on.

Owen’s main point so far has been that the work of mortification is a work of the Holy Spirit that only He can accomplish.  Now he addresses a related point by way of a question:

Why are we exhorted to mortify sin if only the Spirit can mortify Sin?

 In other words, why can’t we just leave the whole work of sanctification to Him?

  •  This work is not different than all the other graces and enablings of the Spirit in us.  He is at work behind all the things we are commanded to do.  He ‘works in us to will and to do of his own good pleasure’.  We are exhorted to do things like pray, but the Spirit is the One at work in us to accomplish what is commanded.  
  • The work of the Spirit is such that our obedience is still required.  He does not override our wills.  ‘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.’

Owen then emphasizes that we are not intended to fight sin by ourselves with our own resources.  To be convicted of sin is the job of the law, but it cannot free us from bondage to sin.  It only condemns.  To think we can ‘keep down sin’ ourselves without the Spirit’s empowering is to enter into ‘the saddest warfare that any poor creature can be engaged in.’  We can never win.  Sin may seem to be knocked down but really we have just stirred up our own fears, sorrows and anguish over the sin to the point that we can no longer see the sin. Meanwhile, it stands unweakened.  Our labor and striving is pointless without the Spirit. 

Owen closes with a question.  If such is the sad state of those who are at least trying to fight sin, what will be the state of those who don’t even care about their sin and don’t mind living under its dominion, whose greatest concern is to gratify their flesh?



And that’s Chapter Three! I don’t know about you, but I’m getting tired of talking and thinking about sin! And I’m very grateful that the Spirit is the one ultimately responsible for my sanctification!  Yes, it’s up to me to co-operate, to follow His lead, but it’s not up to me to forge a path of reformation for myself.  I would like to see more clearly in my own practice, what is the Spirit and what is the flesh.  I’d like a formula to determine this. Any ideas?!  (Or is that just my natural desire to walk by a method and not by faith?!)

 It’s a hard one to swallow that all our effort to suppress sin is in vain if the Spirit is not working through it and directing the process.  But it makes sense–‘whatever is not of faith is sin’.  Fleshly flailings aren’t based in faith, aren’t focused on Christ’s sufficiency and are usually tainted with pride (I’ll do better next time. I’ll try harder.  I can do this! Look, I’m getting better!)  The Gospel is about “I can’t do this; I need a Saviour”.  Funny how all that changes after we’re ‘saved’ so that we commence to live the Christian life by methods and efforts.  

I have been reading Colossians this week:  “Therefore as you have received Christ Jesus the Lord, so walk in Him, having been firmly rooted and now being built up in Him and established in your faith, just as you were instructed, and overflowing with gratitude.” Col.2:6-7 NASB

There are two reminders I need from this passage:  

One, I  received Christ by faith, not by trying hard to be good, and that is precisely how I am to continue to walk in Him–by faith, by receiving to my account His righteousness and by faith dying to the part of me that wants to do my will, not God’s. I have to trust the Spirit will lead me in the particulars.  There is no point in trying to figure out for myself where and how to start!   

And Two, I need this positive focus: ‘overflowing with gratitude’.  All this talk of sin and how to overcome it can become a negative discouraging focus, especially when I take it upon myself as something to figure out how to do. But this verse reminds that we are being built up in Christ as we trust Him with our growth just as we did for our salvation.  And the response expected is not one of grovelling because we still sin, but of rejoicing that we are accepted in Christ; He has met the righteous requirements of the law on our behalf. (Rom.8:3) This is cause for overflowing gratitude, even if we still sin daily.

We who are followers of Christ are in Good Hands.  We have the Spirit as our Helper: “But the Helper, the Holy Spirit, whom the Father will send in my name, he will teach you all things and bring to your remembrance all that I have said to  you…When the Spirit of truth comes, he will guide you into all the truth.” Jn14:26; 16:13





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