The Indwelling Holy Spirit


The Indwelling Holy Spirit

Genevan Institute for Reformed Studies
by Bob Burridge ©2015

God has made a provision for our spiritual growth and encouragement by assuring us of his presence in the person of the Holy Spirit. This presence of God is one of his great covenant promises.

In Exodus 29:45 God affirmed this promise to those who were then his people. He said, “I will dwell among the people of Israel and will be their God.” Jesus Christ was called Immanuel which means “God with us”. Before his crucifixion Jesus promised his disciples that he would send the Holy Spirit to minister to them. Paul wrote to the Romans about this special indwelling presence of the Holy Spirit which is there to enable them to grow in their new life in Christ.

There is a sense in which God dwells among us and in us.

Romans 8:9-11, “You, however, are not in the flesh but in the Spirit, if in fact the Spirit of God dwells in you. Anyone who does not have the Spirit of Christ does not belong to him. But if Christ is in you, although the body is dead because of sin, the Spirit is life because of righteousness. If the Spirit of him who raised Jesus from the dead dwells in you, he who raised Christ Jesus from the dead will also give life to your mortal bodies through his Spirit who dwells in you.”

The Bible uses language saying that believers have the Holy Spirit “dwelling (living) in them”. The primary Greek verb used in this passage is “oik-e-o” (οἰκέω). It is the normal word used then for living in a house, dwelling in a place you consider your home. Another related Greek word “enoik-e-o” (ἐνοικέω) is used also. Its focus is on the actual inhabiting or living in a home. It adds the prefix “en” (ἐν) which is a preposition meaning “in”. So we say this is an “indwelling” of the Holy Spirit among believers and in each individual believer.

This provision of God is not just an empty fact. It produces many benefits for God’s Children. It gives them hope of present comfort and of future resurrection. The actual nature of indwelling is not as easily understood as the fact of it. It is important that we know what it is that God says we have.


The Holy Spirit does not come into some place where he had not been before.

God is everywhere, altogether, always. He fills all space in the universe he created.

Psalm 139:7-10, “Where shall I go from your Spirit? Or where shall I flee from your presence? If I ascend to heaven, you are there! If I make my bed in Sheol, you are there! If I take the wings of the morning and dwell in the uttermost parts of the sea, even there your hand shall lead me, and your right hand shall hold me.”

There is no place where any person of the Trinity is ever absent. He is inside and all around the believer and the worst infidel or pagan. While we are alive or when we die God is there. This “indwelling” of the Holy Spirit can have nothing to do with a physical or spiritual location.

However, God does manifest himself differently in different places while still being altogether present in all of them all the time. When we say God is in Heaven, it doesn’t mean he is absent from everywhere else. It means that there he displays his glory in a special way. In Hell he manifests his justice and wrath. In the elements of the Lord’s Supper God shows his work as Redeemer.

Indwelling begins when a person is redeemed. It does not tell us where the Holy Spirit is. It has to do with that special blessing and relationship a child of God bears with his Redeemer and Lord. Not everyone is indwelt by the Holy Spirit. Jude 19 tells us, “It is these who cause divisions, worldly people, devoid of the Spirit.”

To know accurately what this “indwelling” describes, all the verses in the Bible that mention the Spirit “dwelling in” someone had to be carefully analyzed to see what this relationship produces in the redeemed person. It is not surprising that most of the helpful verses are in the New Testament. It is not that the Holy Spirit’s work was absent in the Old Testament, nor that Old Testament believers had to get along without Him. Since they were “totally depraved” as we are, they could not have done what they did aside from the work of the Holy Spirit. But, before the finished work of the Messiah, the presence of God was known to the average believer mostly through Prophets, symbols and ceremonies. After the figures and symbols were brought to completion in Christ a more direct understanding became possible.


The Spirit’s indwelling produces valuable qualities in the believer.

Notice the Holy Spirit’s involvement in each of these qualities:

The Spirit maintains spiritual life in the redeemed.

Romans 8:9-11, “You, however, are not in the flesh but in the Spirit, if in fact the Spirit of God dwells in you. Anyone who does not have the Spirit of Christ does not belong to him. But if Christ is in you, although the body is dead because of sin, the Spirit is life because of righteousness. If the Spirit of him who raised Jesus from the dead dwells in you, he who raised Christ Jesus from the dead will also give life to your mortal bodies through his Spirit who dwells in you.”

The work of Jesus Christ removes the guilt that separates us from fellowship with God. That separation is the “spiritual death” which is replaced by a living relationship with our Creator. Those made alive by the Spirit are made able to sincerely honor God in their thoughts, words and deeds. The changed life proves that their sonship with God is genuine. Their joy is not sought only in the flesh (the physical realm which can be seen and felt), they also see the spiritual side of things. This assures them that they are not merely living things, they are redeemed creations of a living God.

The Spirit gives spiritual understanding.
The fallen are devoid of spiritual understanding. Romans 3:11, “no one understands; no one seeks for God.” (quoted from Psalm 14)

The indwelling Spirit gives that spiritual understanding which we otherwise could not have.

1 Corinthians 2:12-14, “Now we have received not the spirit of the world, but the Spirit who is from God, that we might understand the things freely given us by God. And we impart this in words not taught by human wisdom but taught by the Spirit, interpreting spiritual truths to those who are spiritual. The natural person does not accept the things of the Spirit of God, for they are folly to him, and he is not able to understand them because they are spiritually discerned.”

Jesus Christ, working by the Spirit which he puts in us when he saves us, enlightens our minds.

Ephesians 3:17-19, “so that Christ may dwell in your hearts through faith–that you, being rooted and grounded in love, may have strength to comprehend with all the saints what is the breadth and length and height and depth, and to know the love of Christ that surpasses knowledge, that you may be filled with all the fullness of God.”

The Spirit Enables us to obey God.
The Spirit in us begins the process of making us holy in practice and thought. This is that progressive sanctification that grows to make us more and more like our Savior, though never fully reaching that perfection in this earthly life. Romans 8:9 reminds us, “You, however, are not in the flesh but in the Spirit, if in fact the Spirit of God dwells in you. Anyone who does not have the Spirit of Christ does not belong to him.” The indwelling work of the Spirit is the opposite of being “in the flesh.” The spiritual dimension of our human life is restored.

Gives assurance of sonship and of salvation
Only the indwelling Spirit gives us true assurance of God at work in our lives.

Romans 8:15-16, “For you did not receive the spirit of slavery to fall back into fear, but you have received the Spirit of adoption as sons, by whom we cry, “Abba! Father!” The Spirit himself bears witness with our spirit that we are children of God,”

This internal testimony of the Holy Spirit does not come by hearing voices or by seeing visions. It comes as the Spirit bears witness to us through God’s written word, and as we see him transform our thoughts, words and activities. The Bible gives us no promise that we will receive private revelations from God. It abundantly speaks of knowing we are his because by his work of grace we learn and keep his commandments. (John 14:12,15,21, 1 John 2:3-6, James 2:17, etc.)

Our Creator produces in us the evidences of understanding, conviction of sin, godly enablement, and thankful obedience. These remove any continuing doubt that we are his. Even the deep grief we experience when we sin is proof that we are changed by grace. 1 John 4:13, “By this we know that we abide in him and he in us, because he has given us of his Spirit. ”

The indwelling Spirit is the seal of genuineness from God. It produces comfort and assurance in the heart of the believer. In his Second Epistle to the Corinthians Paul wrote, “And it is God who establishes us with you in Christ, and has anointed us, and who has also put his seal on us and given us his Spirit in our hearts as a guarantee” (1:21-22), and “He who has prepared us for this very thing is God, who has given us the Spirit as a guarantee” (5:5). Then in Galatians 4:6 he again reminds us that it is the Spirit in us that makes us cry out as children saying, “Abba! Father!”

The indwelling Spirit gives us an eternal hope that cannot fall short or ever fail. He is the conveyor of spiritual life from God (Romans 8:11), a life that is eternal. He is the down-payment of the promise that we will live in the house of the Lord forever.

That is the confidence we have which Paul explained in his letter to the churches in Ephesus. In Ephesians 1:13-14 he wrote, “In him you also, when you heard the word of truth, the gospel of your salvation, and believed in him, were sealed with the promised Holy Spirit, who is the guarantee of our inheritance until we acquire possession of it, to the praise of his glory. ” Then in 4:30, “And do not grieve the Holy Spirit of God, by whom you were sealed for the day of redemption.” It is the Holy Spirit who assures us of the promise that even our physical bodies will be glorified one day.

The Holy Spirit puts the love of God into our hearts.
Romans 5:5, “and hope does not put us to shame, because God’s love has been poured into our hearts through the Holy Spirit who has been given to us.” This is also a source of further assurance that we have been redeemed. 1 John 4:12-13, “No one has ever seen God; if we love one another, God abides in us and his love is perfected in us. By this we know that we abide in him and he in us, because he has given us of his Spirit.”

The Holy Spirit Ministers comfort to God’s children
In John 14:16 Jesus said, “I will ask the Father, and he will give you another Helper, to be with you forever.” The word translated there as “Helper” is the Greek word, “paraclaetos” (παράκλητος) which is someone called alongside to comfort, advise, or give counsel. This is one of the works of the Holy Spirit at work in our lives. Acts 9:31 says, “So the church throughout all Judea and Galilee and Samaria had peace and was being built up. And walking in the fear of the Lord and in the comfort of the Holy Spirit, it multiplied.”

The Psalms are filled with verses about the peace and comfort God the Spirit brings to his children. An example is seen in Psalm 139:7-10, “Where shall I go from your Spirit? Or where shall I flee from your presence? If I ascend to heaven, you are there! If I make my bed in Sheol, you are there! If I take the wings of the morning and dwell in the uttermost parts of the sea, even there your hand shall lead me, and your right hand shall hold me.”

The Holy Spirit strengthens us inwardly and intercedes for us.

Ephesians 3:16, “that according to the riches of his glory he may grant you to be strengthened with power through his Spirit in your inner being,”

Romans 8:26, “Likewise the Spirit helps us in our weakness. For we do not know what to pray for as we ought, but the Spirit himself intercedes for us with groanings too deep for words. “

There are three “groanings” in that Romans context: material creation groans (8:18-22), the believer groans (8:23-25), and the Holy Spirit that dwells in us groans (8:26-27). Some have attempted to use that last reference to support speaking in tongues or literal groaning sounds that come from believers having some higher level spiritual experience. But that is not supported by the context or the fundamental meaning of that word.

The word often translated as “groanings” here is a plural form of the noun “stenagmos” (στεναγμός), which comes from the verb “stenazo” (στενάζω). It refers to something being “narrow” or “restricted”. From this word we get our modern medical term “stenosis” which describes some body area such as a heart valve becoming stiff or closing up causing the flow of blood through it to become restricted. In Paul’s time it came to be used not so much of a verbal “moaning” but more of the anguish of strained emotions. A modern counter part would be the drained emotional feeling as if we’ve been “pulled through a key-hole.”

Creation does not make physical groaning sounds, neither does the Holy Spirit. Creation longs for the completion of God’s redemptive plan. Believers “groan inwardly” (8:23) as we who possess the “first fruits of the Spirit” long eagerly for the fullness of our adoption as God’s children and the redemption of our bodies. The Holy Spirit understands the agony we experience in our still fallible and sinful hearts. So the Spirit intercedes for us as he brings us through those difficult times.


Believers are often said to be “filled” with the Holy Spirit.

All our abilities are gifts of God. He enables us to carry out our callings in life, to grow spiritually, and to do it all for the Glory of God rather than for our own advancement. When the Spirit directs our lives to accomplish what God has called us to do, the Bible at times calls it a “filling” of the Holy Spirit.

Exodus 28:3, “You shall speak to all the skillful, whom I have filled with a spirit of skill, that they make Aaron’s garments to consecrate him for my priesthood.”

Exodus 31:3 where God says of Bezalel, “and I have filled him with the Spirit of God, with ability and intelligence, with knowledge and all craftsmanship”

Micah 3:8, “But as for me, I am filled with power, with the Spirit of the LORD, and with justice and might, to declare to Jacob his transgression and to Israel his sin.”

Deuteronomy 34:9 speaks of Joshua who was filled with the “spirit of wisdom” to lead the people.

Paul reminded Timothy that his talents and opportunities had been given to him by God. In 2 Timothy 1:14 he wrote, “By the Holy Spirit who dwells within us, guard the good deposit entrusted to you.”

In the Bible this filling with the Holy Spirit is often compared with the influence of drinking too much wine. When a person comes under the influence of alcohol he behaves in a way that is different from his natural ways. The Spirit directs us to behave in a more godly manner contrary to how we would behave on our own. A direct comparison is made in Ephesians 5:18, “And do not get drunk with wine, for that is debauchery, but be filled with the Spirit”

This ability of the Holy Spirit to change our behavior is also made clear by the observations of those at Pentecost in Acts 2:4, “And they were all filled with the Holy Spirit and began to speak in other tongues as the Spirit gave them utterance.” (compare with Acts 2:13, “But others mocking said, ‘They are filled with new wine.’ “).

The primary verb for “being filled” in these passages is “plaero-o” (πληρόω). It means to fill something, to fill someone with certain powers or qualities, to bring something to completion (fulfill). The noun form “plaeroma” (πλήρωμα) is that condition of fullness. [see entries in Bauer, Arndt & Gingrich “Greek-English Lexicon”]

King David did not want to lose the enablement of the Spirit to rule God’s people as their king. He saw that happen to King Saul after his rebellion against God. When David sinned with Bathsheba, lied to cover it up, and had her husband killed, he prayed in Psalm 51:10-12, “Create in me a clean heart, O God, and renew a right spirit within me. Cast me not away from your presence, and take not your Holy Spirit from me. Restore to me the joy of your salvation, and uphold me with a willing spirit.”

Any God-honoring success in whatever we do in life, is provided by the work of the Spirit in us.


The Spirit’s indwelling is not unique to the New Testament church.

The same qualities the Holy Spirit is said to produce by dwelling in and among believers after the finished work of Christ are also attributed to believers in the Old Testament.

Assembling the many verses about the work of the Holy Spirit in the life of the New Testament era believer we see that he enlivens, helps, enables, comforts, and strengthens them. He confirms, seals, and assures them of salvation and of the covenant promises. He intercedes for them, gives understanding, rules in their hearts, marks them out as his people, stirs love in their hearts, and makes them grow in godliness.

How could fallen, totally depraved Old Testament believers have experienced these covenant blessings if it was not also an operation of the Holy Spirit in their hearts? An example of direct statements about this Old Testament era “indwelling” is Numbers 27:18 where Joshua was called, “… a man in whom is the Spirit.”

The coming of the Holy Spirit at Pentecost in Acts 2 does not mean he came into a place he had not been before. God is altogether always everywhere.

When Jesus promised to send the Holy Spirit to be a special “comforter” or “helper” to his church after he left (John 14:26, 15:26, 16:7), this could not mean the Spirit did not comfort believers before that time. The Bible shows clearly that he did. The difference was that instead of ministering these covenant blessings through priests, temple rituals, and blood sacrifices, believers understood what those things all pointed toward, the completed work of the Savior as the archetype High Priest, the Lamb of God. The Spirit would now operate directly upon the individual apart from these Old Testament symbols and types. He would teach his people directly from a completed Bible instead of through individual Prophets sent with specific messages from God.

Pentecost also marked God’s judgment upon apostate Israel and the expansion of God’s Kingdom to include the Gentiles as predicted by the ancient Prophets. By comparing Acts 2 (quoting Joel 2) with warnings such as Deuteronomy 28:49 and Isaiah 28:11 this evident meaning of the first century “speaking in tongues” becomes clear (see an expanded study of this in “A Study of Speaking in Tongues”). Pentecost was not the beginning of “indwelling”. That has always been the treasure of believers.

The presence of God in and among his people has always been a central promise of the Covenant of Grace. Repeatedly God’s people were assured that God would dwell among them and be their God (Exodus 29:45, Leviticus 26:12, Ezekiel 37:27, etc.).

Paul quoted this Old Testament promise when he wrote 2 Corinthians 6:16, “What agreement has the temple of God with idols? For we are the temple of the living God; as God said, ‘I will make my dwelling among them and walk among them, and I will be their God, and they shall be my people.’ ”

Thanks be to our faithful covenant God who in this age has given us a more full understanding of the symbols fulfilled in the coming of the promised Messiah. He now ministers more directly in the hearts of his people granting them the benefits of His living presence. This Holy Spirit indeed dwells within. We are never alone.

Note: Bible quotations are from the English Standard Version unless otherwise noted.

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