Theology Basics: The Indwelling of the Holy Spirit

A hugely important, though often overlooked, element of the Christian faith is the simple truth that once someone has put their faith in Jesus for the forgiveness of their sins and been born again (John 3:3-8), the Holy Spirit enters into the person and dwells inside of them.

In theology we call this the indwelling of the Holy Spirit, and although it often goes underappreciated, this theological truth changes everything for the believer.

Who is the Holy Spirit?

The doctrine of the trinity is a complex topic, far outside the scope of this article. But to briefly summarize, the God who has revealed himself throughout human history, and has intervened in history to bring about salvation, is what we call a triune God. He is distinctly one God, so the Christian faith is inherently monotheistic (worshipping one God). Scripture is clear that there is only one God whom we must worship, and it is the God of the Jewish and Christian faiths.

But what is unique about God is that there are three distinct persons who are simultaneously one. God the Father is God. Jesus the Son, took on human flesh and lived among us as fully human and yet fully God (another complex topic to tackle another time). And the Holy Spirit, which was the promised helper and advocate sent after Jesus’ ascension, is also fully God.

For our purposes, it is important to recognize that the Holy Spirit, which God sent to aid those who follow him, is every bit as much God as God the Father and Jesus the Son. The Holy Spirit is not an impersonal force (like “the force” in Star Wars), he is not God’s plucky little side-kick. The Holy Spirit is a person and he is fully God. All the attributes that make God God are attributes of the Holy Spirit. Believers too often fail to recognize the magnitude of God himself dwelling inside of them and assisting them with their Christian walk.

Why Indwelling?

To really understand the reason for the Holy Spirit taking up residence inside of our hearts, we first must recognize the condition we are in apart from God’s grace through Jesus Christ.

The problem of sin is real, and because of it every human being is born in a state of spiritual death. On our own we are incapable of a relationship with God. There are hints, biblically, that we are not even capable of putting our faith in Christ unless God first draws us to him through the conviction of our sins, which is done by the Holy Spirit (John 6:44; John 16:8). Outside of the work of God externally on our lives, we are by default born spiritually dead (Ephesians 2:1-3).

Our sin separates us from God, and throughout the Old Testament God provided a sacrificial system in which animals could be killed in our place in order to pay the due penalty for our sin while continuing to live. This sacrificial system pointed forward to how Jesus would ultimately come, sinless and innocent, and suffer in your place on the cross for your personal sins. What Jesus suffered, you deserved, and since Jesus willingly took your punishment in your place, in God’s eyes when you recognize your sin and submit to Jesus’ authority in your life, your sinful record is swapped out for Jesus’ perfect, sinless record. We call this the substitutionary atonement.

It is a free gift from God, who does not require any works to earn it, but requires that one allow Jesus to have authority in their life and to turn away from their sin and follow Jesus instead. This redemption was made possible by God himself taking on human flesh, and doing for us what we were unable to do for ourselves (because he alone was both fully human and fully God).

When the Holy Spirit convicts us of our sin and calls us and we respond positively to the gospel message, desiring to have new life with Christ and to turn away from our fallen sinful brokenness, a few things happen.

In that moment, our old, sinful self is put to death, metaphorically crucified with Jesus on the cross. You might imagine yourself nailed up to the cross with Jesus as he suffered. Then, because of the substitutionary nature of Jesus’ suffering, having died to your sin, you rise again vicariously with Jesus in his resurrection on the third day (Romans 6:1-11).

This very thing that happens when one puts their faith in Jesus is what Jesus himself describes about the need for spiritual birth.

Jesus answered him, “Truly, truly, I say to you, unless one is born again he cannot see the kingdom of God.”  Nicodemus said to him, “How can a man be born when he is old? Can he enter a second time into his mother's womb and be born?” Jesus answered, “Truly, truly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God. That which is born of the flesh is flesh, and that which is born of the Spirit is spirit. Do not marvel that I said to you, ‘You must be born again.’ The wind blows where it wishes, and you hear its sound, but you do not know where it comes from or where it goes. So it is with everyone who is born of the Spirit.”

John 3:3-8 ESV

This is what we refer to when people talk about being a “born again Christian.” But it goes deeper than that. The thing that allows the newly converted Christian to come to a saving faith at all is that the Holy Spirit has convicted them and they have responded positively.

What happens, when a person comes to a saving faith in Jesus, is that the Holy Spirit enters into them. This is what causes the spiritual birth, this is what brings them from a state of spiritual death into life. The indwelling of the Holy Spirit and salvation are the same thing!

So far we have been talking only about the Holy Spirit’s role in salvation, but the point of salvation and entrance into eternal life is only the beginning of the Christian walk.

The Benefits of the Holy Spirit

The benefits of the indwelling of the Holy Spirit are practical and many. When the Holy Spirit (who – you’ll remember – is God himself) moves in, part of the new life you’re given is that he works in your heart to bring about change and beings to transform you, little by little, into someone more like Jesus himself. We call this process sanctification, and it is a lifelong process.

Sin is still present and will continue to be a reality until we are on the other side of eternity, but because you’re a new creation, you will find that sin that used to come naturally will, over time, become detestable. You find yourself unable to engage in the sinful activity you once lusted after, because you’re being transformed by God himself from the inside out.

The Holy Spirit, in this way, functions in the life of a believer as a sort of conscience. People describe a still small voice, nudging you and convicting you when you have acted sinfully. Gradually, over time, you become transformed. It is not as though the Holy Spirit overrides your mind and uses you as a puppet, you are still the one making the decisions, but you are helped and guided by God himself who now dwells within you.

The Fruit of the Spirit is a laundry list of the fruits (the outward working in your life) of having the Holy Spirit dwelling inside of you (Galatians 5:16-25).

Another benefit that the Holy Spirit provides, which works hand in hand with our sanctification, is that he guides us to a deeper knowledge of God (John 16:12-15). This is a beautiful truth, because the primary way we, as modern believers, experience God and get to know him is by reading and study his Word.

The Bible is complicated, and there is a lot going on, but the beautiful thing is that for the believer, we are not just left to scour the written Word on our own and try to puzzle out who God is and how we should live in response to the gospel. God himself, who lives inside of us as the Holy Spirit, explains Scripture to us when we engage with it humbly and openly.

When we want to know God on a deeper level and we turn to Scripture, he reveals how it points to himself. I think this is in some part what the writer of Hebrews means when he asserts that Scripture is God’s Word alive and active (Hebrews 4:12).

The benefits of living with the Holy Spirit are profoundly powerful when we realize what we are talking about. There is an interesting parallel between Jesus’ saving work on the cross (and the uniqueness of his being God dwelling among us in human form) and the indwelling of the Holy Spirit as God himself dwelling inside of us to effect the necessary changes in our lives to turn away from sin and live into the faith he has called us to.