The Holy Spirit’s Work in Sanctifying the Believer
In writing his first letter, the apostle Peter set a high standard for those who have received the grace of God. At 1 Peter 1:15, 16 we read: “But just as he who called you is holy, so be holy in all you do; for it is written: ‘Be holy, because I am holy.'” For human beings who are born with a sinful nature, that is a tall order. In fact, it is impossible in our own strength. Fortunately, God has made the way for believers in Jesus Christ to become completely holy, first in a legal sense and later in actuality. This work of God in a believer’s life is carried out by the third Person of the Trinity, the Holy Spirit.
The operative word in the above statements is “believer.” The life of faith begins when one places faith and trust in Jesus Christ as Lord and Savior, repenting of sin and beginning a life course of obedience to God. It is at this point of faith that one is “born again” (regenerated) and “saved,” the latter in the sense of being delivered from the penalty of sin and being granted eternal life as a child of God (John 1:12; 3:3-8; 10:27-29). While this step of faith is taken in the will of the believer, it is empowered by the Holy Spirit, and is thus a work of God in the life of the individual. The apostle Paul wrote: “For it is by grace you have been saved, through faith-and this not from yourselves, it is the gift of God – not by works, so that no one can boast. For we are God’s workmanship, created in Christ Jesus to do good works, which God prepared in advance for us to do” (Ephesians 2:8-10) [emphasis mine]. Our salvation is God’s gift and His work, not ours. The result of that salvation is “good works.”
Another phenomenon that occurs at the time of initial salvation is what the New Testament calls the “baptism of the Holy Spirit” (Matthew 3:11; Acts 1:5; 11:16). Thiessen states that “this baptism takes place at the moment of salvation,” and Grudem defines it as “coming into the new covenant power of the Holy Spirit. This would include the impartation of new spiritual life (in regeneration), cleansing from sin, a break with the power and love of sin, and empowering for ministry.”
When we place faith in Christ, God justifies us, declaring us righteous in a legal sense on the basis of imputing Christ’s righteousness to us (Romans 4:6; 5:17). Also at this point, the Holy Spirit actually begins to indwell the believer as a constant presence (John 14:16, 17; 1 Corinthians 3:16; 6:19). However, even after salvation, we are still sinners in fact and remain so throughout our earthly lives. Yet God saves us with the intent of ultimately making us holy in actual fact. This tells us something about the nature of faith that brings initial salvation. Saving faith in Christ is not mere intellectual assent to the facts about Him. It is a placement of our full trust in Him accompanied by a willingness to turn from sin and to live obediently as the Holy Spirit empowers us. While salvation is by faith alone, “faith by itself, if it is not accompanied by action, is dead” (James 2:17). Real, saving faith is always accompanied at least to some degree by good works and spiritual growth in the life of the believer.
Throughout our lives, the Holy Spirit works in us to make us more like Jesus Christ. The name that theologians give to this process is sanctification. To the believers at Philippi, Paul wrote: “In all my prayers for all of you, I always pray with joy because of your partnership in the gospel from the first day until now, being confident of this, that he who began a good work in you will carry it on to completion until the day of Christ Jesus” (Philippians 1:4-6). This text demonstrates that our initial salvation as well as the spiritual development that follows it is the work of God in our lives, a work that will only be fully completed at “the day of Christ Jesus.”
The goal of this work of the Holy Spirit is a perfected church as the glorified bride of Christ: “Husbands, love your wives, just as Christ loved the church and gave himself up for her to make her holy, cleansing her by the washing with water through the word, and to present her to himself as a radiant church, without stain or wrinkle or any other blemish, but holy and blameless” (Ephesians 5:25-27).
The Believer’s Dilemma
The problem for the believer is that the sin nature is not removed at the time of initial justification. God has given us a new nature, but it is at war with the old nature of sin, which Paul calls “the flesh” (Romans 7:5, 18, NASB). Paul found himself distressed by the war between these two natures in his life:
“For I know that nothing good dwells in me, that is, in my flesh; for the willing is present in me, but the doing of the good is not. For the good that I want, I do not do, but I practice the very evil that I do not want. But if I am doing the very thing I do not want, I am no longer the one doing it, but sin which dwells in me. I find then the principle that evil is present in me, the one who wants to do good. For I joyfully concur with the law of God in the inner man, but I see a different law in the members of my body, waging war against the law of my mind and making me a prisoner of the law of sin which is in my members” (Romans 7:18-23).
There was a very real conflict going on within Paul’s spirit. On the one hand, the “flesh,” the fallen sinful nature that remained within him, drew him to sin. And yet, the new nature that God had given him struggled against this sin. The result was that Paul could no longer be comfortable with his sin, even though he continued to sin at times. In his mind and heart, he wanted to refrain from sin, but was unable to do so fully. Nonetheless, victory was available to him despite his frustration, since he next writes:
“Wretched man that I am! Who will set me free from the body of this death? Thanks be to God through Jesus Christ our Lord! So then, on the one hand I myself with my mind am serving the law of God, but on the other, with my flesh the law of sin” (Romans 7:24, 25).
By his faith in Jesus Christ and through the power of the Holy Spirit, Paul was able to gain victory over sin, even though he would never be completely sinless in this life. His attitude toward sin, however, was completely the opposite of what it had been before his coming to know Christ as Savior.
A Cooperative Work
Baker points out four ways in which the Holy Spirit works in the lives of believers to bring about an increasing degree of holiness throughout their lives. Each of these is worthy of brief consideration here:
1. The Holy Spirit “Sets His Desire Against the Flesh.” This phrasing is taken from Galatians 5:16, 17, which says: “But I say, walk by the Spirit, and you will not carry out the desire of the flesh. For the flesh sets its desire against the Spirit, and the Spirit against the flesh; for these are in opposition to one another, so that you may not do the things that you please.” This echoes Paul’s dilemma in Romans 7 as cited above. Two natures are at work within the believer. The “flesh,” or sinful nature, draws us to sin, but the Spirit of God within us resists sin by defining sin and convicting us of it when we commit sin. Apart from Christ, we had no awareness of sin, but the indwelling Holy Spirit creates a new sensitivity that opposes the sin nature. Because the two natures are in opposition to each other, there is, in effect, a “stalemate” that needs to be broken.
2. The Holy Spirit Empowers the Believer to Obey God. The believer is not without responsibility in the matter of his or her sanctification. Breaking the “stalemate” that exists between the two natures requires effort on the part of the believer that is empowered by the Spirit. Paul admonished the Galatian believers to “walk by the Spirit, and you will not carry out the desire of the flesh” (Galatians 5:16). Baker explains that “walking by the Spirit is living in conscious reliance on Him to enable me as I choose to do what is right.” The power comes from the Holy Spirit, but the choice must be ours. We need to “set our mind on the Spirit,” allowing Him to have His way with our lives (Romans 8:5, 6). What is different for us as believers is that we have the ability to make the choice, in effect, the ability to say “no” to sin. This is an option that was not open to us before we knew Christ.
3. The Holy Spirit Imparts Spiritual Truth and Wisdom to the Believer. Jesus told His apostles before His death that “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 said to you” (John 14:26). It is by means of the Holy Spirit that believers are able to understand the Word of God and to apply it to their lives. Paul wrote that unbelievers do not have the ability to understand the Gospel, because “the god of this world has blinded the minds of the unbelieving so that they might not see the light of the gospel of the glory of Christ, who is the image of God” (2 Corinthians 4:4). When the Spirit begins our new spiritual life, He also gives us the ability to know and understand God’s will and truth as revealed in the Bible.
Some Christians would extend this point even further and claim that the Holy Spirit gives direct guidance in everyday matters of decision making. While we should not limit God’s ability to prompt us in any way He chooses, the Scriptures do not appear to support this as a routine mode of the Spirit’s operation. Christians are to be guided first and foremost by the Word of God in our lives, not by subjective impressions that we may perceive as originating with the Spirit. The danger in such subjectivism should be obvious: we are prone as sinful beings to self-deception, and it is very easy for us to attribute our own thoughts and desires to God. Certainly, if anyone believes that he or she has received a prompting from God, it must be recognized that Scripture is supreme, and is the standard by which all other impressions are to be tested (1 Thessalonians 5:21; 1 John 4:1).
4. The Holy Spirit Produces Christ-Like Character in the Believer. Under the Holy Spirit’s empowering, believers have the option not to sin when confronted by temptation. As noted above, “walking in the Spirit” enables us to draw upon the Spirit’s power coupled with our own choice to avoid sin. By living consistently in this manner, we are “filled with the Spirit” in the sense of being under His constant control or influence (Ephesians 5:18-21). As we live in this manner, the Spirit will, day by day throughout our lives, make us more like Jesus Christ in holiness. More and more, we will forsake the sinful ways of the old nature and manifest in our lives the “fruit of the Spirit [which] is love, joy, peace, patience, kindness, goodness, faithfulness, gentleness and self-control. Against such things there is no law” (Galatians 5:22, 23).
The use of the term “fruit” in the above text makes an interesting point. Some legalistic groups admonish their followers to work hard at manifesting the fruit of the Spirit by trying to demonstrate love, joy, peace and so on in their lives. This is putting the cart before the horse. We do not gain the Holy Spirit by working hard at developing these qualities; we manifest these qualities because the Spirit is doing His work within us and changing us from the inside out. Nobody has ever seen an apple tree struggle and strain, working hard to produce apples. It is the very nature of a healthy apple tree to produce apples; if an apple tree does not produce apples, there is something wrong with it. It is similar with the fruit of the Spirit. If the Holy Spirit is doing His work in our lives, making us daily more like Jesus, we will naturally produce the qualities that Paul describes, because these qualities are His characteristics. We do not work at manifesting the outward qualities; rather, we cooperate with the work of the Spirit by following His leading in everything, and the outward evidence follows naturally.
“Just As He Is Pure”
The Christian life is lived in anticipation of the day when Christ will appear and when believers will “be like him, for we shall see him as he is” (1 John 3:2). At that time, believers will be glorified by the Holy Spirit and miraculously made like Christ, immortal, incorruptible and without sin (1 Corinthians 15:53, 54). The quest to become more like Jesus in this life is a joint work of the believer and of the Holy Spirit dwelling within the believer. The apostle John speaks of the believer’s part in this work when he writes in reference to the hope mentioned above, “Everyone who has this hope in him purifies himself, just as he is pure” (1 John 3:3). John also acknowledged God’s part in this work: “if we walk in the light, as he is in the light, we have fellowship with one another, and the blood of Jesus, his Son, purifies us from all sin” (1 John 1:7).
Lest we think that there are two separate works in progress or that we in some manner contribute to our own holiness through our works, Paul clarifies: “Therefore, my dear friends, as you have always obeyed – not only in my presence, but now much more in my absence – continue to work out your salvation with fear and trembling, for it is God who works in you to will and to act according to his good purpose” (Philippians 2:12, 13) [emphasis mine].
The “working out” of our salvation - the good works that we perform in appreciation of the immeasurable gift that God has given us - Paul says do not spring from our own strength or will. Rather, God works in us, not only to produce the works, but even to bring about the will to do them. Our best efforts are merely a response to the work that God the Holy Spirit has done and is doing in our lives. For every facet of our Christian lives, then, for whatever we accomplish for the Kingdom of God, all praise must be given to Him alone.
Baker, William H. Survey of Theology 1 Study Guide. Chicago, IL: Moody Bible Institute, 2004 rev.
Barker, Kenneth, Gen. Ed. The NIV Study Bible, 10th Anniversary Ed. Grand Rapids, MI: Zondervan, 1995.
Dorman, Ted M. Faith for all Seasons, Nashville, TN: Broadman & Holman Publishers, 2001.
Grudem, Wayne. Systematic Theology: An Introduction to Biblical Doctrine. Grand Rapids, MI: Zondervan, 2000 rev.
Saucy, Robert L. “‘Sinners’ Who Are Forgiven or ‘Saints’ Who Sin?” Bibliotheca Sacra 152 (October-December 1995):Â 400-12.
Thiessen, Henry C. Lectures in Systematic Theology. Grand Rapids, MI: William B. Eerdmans Publishing Co., 1999.
Towns, Elmer L. “Martin Luther on Sanctification.” Bibliotheca Sacra 126 (April-June 1969):Â 115-122.
Zodhiates, Spiros. Hebrew-Greek Key Word Study Bible (NASB). Chattanooga, TN: AMG Publishers, 1990.
 Henry C. Thiessen. Lectures in Systematic Theology. Grand Rapids, MI: William B. Eerdmans Publishing Co., 1999, p. 253.
 Grudem, Wayne. Systematic Theology: An Introduction to Biblical Doctrine. Grand Rapids, MI: Zondervan, 2000 rev. p. 1236.
 William H. Baker, Survey of Theology 1 Study Guide. Chicago, IL: Moody Bible Institute, 2004 rev. pp. 124-5. The four subheadings in this section are taken from this source.