The baptism and indwelling of the Holy Spirit is the New Covenant blessing of the presence and work of the Holy Spirit in the life of a believer.


Promised in prophets for those in the New Covenant, the Holy Spirit has been poured out upon the church by Jesus Christ through the power of his resurrection. The Spirit now brings believers into communion with the Father and the Son through the new birth, fills the believer with the love of God, works holiness in the lives of believers, and convinces people of the truth of the gospel. Believers ought to seek to be continually filled with the Spirit in order to love others through our words and deeds, seeking to build up the church through the gifts Jesus Christ gives to his Church through the Spirit.

God the Holy Spirit is the third person of the Holy Trinity. He is a person and not simply an influence; he is fully God, just as God the Father is fully God and God the Son is fully God. He is eternal. He dwells in perfect fellowship with God the Father and God the Son. In the Apostles Creed we affirm, “I believe in God, the Father … I believe in Jesus Christ … I believe in the Holy Spirit …”

In this article we focus on how and why God the Holy Spirit works in, and upon, human beings. Our study will be in four parts. First, we consider, in the Old Testament, the promise of the Holy Spirit. Next, we ponder the wonder of Jesus Christ, the man of the Spirit. Third, we think about what the Βible teaches about Jesus as the one who baptizes with the Spirit. Finally, we look at the main elements of the work of the indwelling Spirit in the life of the Christian believer.

The Promise of the Holy Spirit in the New Covenant

In the Old Covenant the people of God were given, as a great blessing, the Law of God. This Law is a wise, precious, perfect expression of the character of the Covenant God who redeemed them from slavery in Egypt (e.g. Deut. 4:5–8; see also Rom. 7:12). Male circumcision was the outward sign of the Law; it came with a repeated exhortation to, as it were, “circumcise the heart” (e.g. Deut. 10:16). The people needed the good and perfect Law to be written on their hearts, so that they deeply chose and desired to keep it. This they, like all human beings by nature, failed to do and were not able to do. This is “what the Law, weakened by the flesh, could not do” (Rom. 8:3).

And so repeatedly, first in the Law (e.g. Deut. 30:6) and then in the prophets, the promise was given that the Law would be written on hearts under a new covenant. “I will put my law within them, and I will write it on their hearts” (Jer. 31:33). This writing of the Law on the human heart will be the work of the Holy Spirit. “And I will give you a new heart, and a new spirit I will put within you. And I will remove the heart of stone from your flesh and give you a heart of flesh. And I will put my Spirit within you, and cause you to walk in my statutes and be careful to obey my judgements” (Ezek. 36:26–27). God promises to give his Spirit to all his people (Joel 2:28–29).

In essence, then, the promise is that God will indwell the human heart by his Spirit to bring the holiness of his perfect Law into the heart.

Jesus Christ, the Man of the Spirit

When the eternal Son of God took upon himself a fully human nature in the Incarnation, the Holy Spirit was his constant and intimate companion. The conception of his human body in the womb of Mary was the work of the Holy Spirit (Luke 1:35). At his baptism by John the Baptist the Holy Spirit came upon him in power to equip him for his public ministry (e.g. Luke 3:22; John 1:32–33). Jesus resists temptation by the Spirit (Luke 4:1–13); he engages in public ministry and works miracles by the power of the Holy Spirit (e.g. Luke 4:14; Acts 10:38). It is by the Spirit that Jesus “utters the words of God, for he [that is, God] gives the Spirit [that is, to Jesus] without measure” (John 3:34).

Jesus completely and perfectly is the Man of the Spirit, so much so that the Holy Spirit comes also to be called “the Spirit of Jesus” or “the Spirit of Christ” (e.g. Phil. 1:19; see also Sinclair Ferguson, The Holy Spirit).

Jesus Christ, the Baptizer with the Spirit

In all four gospels John the Baptist contrasts his own baptism with water (an outward and symbolic baptism of repentance) with an awesome heart work to be done by Jesus, which he calls the baptism in, or with, the Holy Spirit (Matt. 3:11; Mark 1:8; Luke 3:16; John 1:33 and cf. Acts 11:16). This at last will be the fulfilment of the Old Covenant promises, that the Spirit of God will indwell human hearts.

But—and this is important—this outpouring must wait until the Son of God has paid the penalty for sinners at the Cross. Using the image of living water, Jesus repeatedly speaks about the Holy Spirit (John 4:10-15; John 7:37, 38). John explains that the Spirit is the one “whom those who believed in (Jesus) were to receive, for as yet the Spirit had not been given, because Jesus was not yet glorified” (John 7:39). This “glory” or “lifting up” in John’s gospel refers supremely to the Cross (e.g. John 12:33). Only when sins are paid for can the Spirit be poured out on all the people of God.

After the Cross and Resurrection, Jesus repeats this promise of a baptism with the Holy Spirit (Acts 1:5 and cf. the anticipatory sign of John 20:22). This baptism happens first, and most dramatically, to the disciples on the Day of Pentecost (Acts 2). Since then, it is the birthright of every believer at the very start of a truly Christian life.

(The Baptism with the Holy Spirit has sometimes been thought to refer to a Christian experience subsequent to conversion, and often associated with the gift of speaking in tongues. But a careful study of the biblical texts demonstrates that it refers to what happens at conversion. A classic study of this question is John Stott’s book Baptism and Fullness, which has persuaded many charismatics and Pentecostals not to use the language of “the Baptism of the Spirit” about a second-stage experience.)

The Ministry of the Indwelling Spirit in the Believer

The Spirit gives new birth and brings the believer into fellowship with the Father and the Son.

The Holy Spirit gives new birth, or a birth from above, which imparts spiritual life into a human being who is, by nature, dead in trespasses and sins (Eph. 2:1-3; John 3:1-8; Titus 3:5). This new birth cannot be engineered by any human instrument, whether by the manipulation of emotions or the persuasion of the mind, for everything which is born of flesh (human instrumentality) will be flesh and not the new life of the Spirit (John 3:6). This birth from above is the sovereign work of the Triune God; it is achieved in the human heart by God the Holy Spirit.

Before Jesus left his disciples to go to the Cross for sinners, he promised them that he would return to them. He did this, temporarily, for a few weeks, in his Resurrection body. But he did it forever in the Person of his Holy Spirit. By the ministry of the Holy Spirit, God the Father and God the Son make their home in the heart of a man or woman who is born again (John 14:15-24). It is by the indwelling Spirit that believers enjoy fellowship with the Father and the Son (e.g. 1 John 1:3).

The Spirit pours the love of God into the heart of the believer.

In the context of sufferings, endurance, character and hope, Paul writes that “hope does not put us to shame, because the love of God has been poured into our hearts through the Holy Spirit who has been given to us” (Rom. 5:5). The expression “the love of God” may mean the love that God shows to us, or the love that we show to God, or both. Probably and primarily it is the love that God shows to us, although it likely includes our responsive love to God. By bringing us into fellowship with the Triune God, the Holy Spirit assures us of the eternal love that God the Father, God the Son, and he himself, God the Holy Spirit, have for his people from all eternity and to all eternity.

The Holy Spirit works holiness in the believer.

The Holy Spirit is holy. He burns with the fiery holiness of the Triune God. Speaking of the baptism of the Holy Spirit, John the Baptist preaches that Jesus “will baptize with the Holy Spirit and with fire” (Luke 3:16). This is a figure of speech called a hendiadys, one truth being spoken in two ways: the Holy Spirit is the fire who burns up the chaff of sinfulness. Because of the Cross of Christ, this burning does not destroy the believer, but purifies him or her.

After conversion, then, one of the deepest ministries of the Spirit in the believer is to engage in a lifelong war against sin within the human heart. Galatians 5:16–26 expresses this most famously and vividly. We are to “walk by the Spirit” even though “the desires of the flesh” (the old nature) continue to strive within us. The most evident mark of the baptism and indwelling of the Spirit in the believer is a life that is increasingly marked by “love, joy, peace, patience, kindness, goodness, faithfulness, gentleness, self-control”.

The Holy Spirit convinces people of the truth of Jesus and leads them to walk in that truth.

In John 13:31 (after Judas Iscariot leaves) until John 16:33 Jesus speaks to the apostles. All of what he says applies immediately to the apostles. For example, in John 14:26 he promises that the Holy Spirit will remind them of what Jesus has said to them and enable them to understand it. He can remind them because they were there to hear it; he cannot remind us in the same way.

Nevertheless, there is a carry-over from the eleven apostles to the apostolic church of Christ. For they are this apostolic church in embryo. We rightly, albeit carefully, apply these chapters to ourselves. In John 16:5–15 Jesus speaks of the work of the Holy Spirit first in the world (verses 8–11) and then to the apostolic church (verses 12–15).

For those of the world the only action the New Testament attributes to the Holy Spirit is to bring conviction. He convinces the world of our sin, about the righteousness of Christ, and about judgment. He does this at the start of the Christian life, at the time of conversion; and he goes on doing this work in the believer, in whom something of “the world” continues to struggle.

To the apostles Jesus promises that the Spirit of truth “will guide you into all truth.” This means teaching them the meaning of the things of Jesus. He unpacks for them, as it were, all the revelation of the Father they have seen in Jesus. As a result, their teaching is recorded for us on the New Testament (which is either written by apostles or by others recording the apostolic teaching).

The Holy Spirit does not lead us into fresh truth; rather, he opens up for us the apostolic church, the perfect revelation of the Father in Jesus to which the New Testament bears testimony. We may pray for, and expect, the Holy Spirit to help us both to understand the biblical truth of Jesus and to give us grace to walk in that truth (see Christopher Ash, Seeing the Spirit).

We should be filled with the Spirit again and again so that He will transform our words and deeds.

Using a present imperative to indicate an ongoing and repeated filling, Paul writes, “be filled with the Spirit” and goes on to expand what that will mean in a succession of participles. The church filled with the Spirit will address one another in “psalms and hymns and spiritual songs” (all three of which mainly refer to biblical psalms); we will do so with all our hearts, for it will be a genuine, and heart-shaping singing of psalms; we will be full of thankfulness to God the Father in the name of the Lord Jesus Christ. And we will live this out by submitting one to another, in the relationships of submission that Paul goes on to teach: Christian wives will show a dignified and godly submission to husbands; Christian children will obey their parents; Christian slaves will choose to serve their masters well. All this is the outworking of the filling of the Holy Spirit.

The Ascended Christ gives the gifts of the Spirit to build up the Church.

Quoting from Psalm 68, in Ephesians 4:7–16 Paul says that the victorious and ascended Christ will give gifts to his people. In this passage he speaks of the foundational gifts of the apostles and prophets (which we know to be the foundations of the church from Ephesians 2:20), and the ongoing gifts of evangelists and pastor-teachers.

These and other gifts are given to his Church by Christ through the ministry of the Holy Spirit. Other passages that refer to such spiritual gifts include 1 Corinthians 12:4–11, 1 Corinthians 14, and Romans 12:3–8. Christians have not always agreed either about what each of these gifts means or about whether or not we should still expect a particular gift to be in evidence today in Christ’s Church.

The Holy Spirit and our longings and prayers

In conclusion, it is important to keep the central truths of the Holy Spirit at the center of our thoughts and prayers. He lives in our hearts that we may walk with Christ and with the Father in holiness and love. Let us pray that the Church of Christ will be filled afresh in each generation by the Spirit of holiness, who is the Spirit of Christ.

Further Reading

This essay is part of the Concise Theology series. All views expressed in this essay are those of the author. This essay is freely available under Creative Commons License with Attribution-ShareAlike, allowing users to share it in other mediums/formats and adapt/translate the content as long as an attribution link, indication of changes, and the same Creative Commons License applies to that material. If you are interested in translating our content or are interested in joining our community of translators, please reach out to us.

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