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Ministries of the Holy Spirit in the Church

We're working through Systematic Theology III, and specifically, the doctrine of the Holy Spirit. We’re now talking about the role of the Holy Spirit in the New Testament.

Last time we talked about conviction and the Holy Spirit -- namely, that one of the primary jobs of the Spirit in the unbelieving world is to bring an objective, judicial conviction of guilt. We spent our time looking at John 16:8-11.

We saw that the Spirit will bring a conviction concerning sin, righteousness, and judgment. So check it out if you didn’t get a chance to listen.

Today we plan to talk about the ministries of the Spirit within the church.

The ministry of the Holy Spirit in the lives of Christians

8 Primary categories:

- The Holy Spirit is the guarantee, the down-payment, the first-fruits, the seal of God’s work in our life. (*And this is an objective reality.)

Eph. 1:13-14 “In Him, you also, after listening to the message of truth, the gospel of your salvation -- having also believed, you were sealed in Him with the Holy Spirit of promise, who is given as a pledge of our inheritance, with a view to the redemption of God's own possession, to the praise of His glory.”

Eph. 4:30“And do not grieve the Holy Spirit of God, by whom you were sealed for the day of redemption.”

The Scriptures are clear that God will complete the work that He begins in our life (Phil. 1:6). The Holy Spirit is the objective guarantee of this ongoing work, but also the guarantee that God will indeed finish the work that He has promised.

Romans 8:23 - “And not only this, but also we ourselves, having the first fruits of the Spirit, even we ourselves groan within ourselves, waiting eagerly for our adoption as sons, the redemption of our body.”

“The first fruits” is a reference to Israel giving the first of their harvest to the Lord.

It was a way to show their devotion to Him. If they gave their first fruits, the promise is that God would abundantly supply them with their needs.

Well in a similar way, God giving us His Holy Spirit is His way of displaying His devotion to us -- to complete His promised work.

It’s a wonderful verse because it is not we who need to give the first fruits, but God!

He gives us the Spirit (“the first fruits”), which also means that He will give us everything else required to save us.

In other words, He does it all!

- The Holy Spirit gives believers assurance of salvation (*And this is a subjective reality).

Rom. 8:16 “The Spirit Himself bears witness with our spirit that we are children of God.”

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.”

This is an inner-subjective confidence that we belong to God forever. It is a gift and wonderful privilege for genuine Christians.

Now, the point to understand, however, is that assurance is a privilege for all Christians, but it is not necessarily a reality for all Christians.

Reasons Christians might lack assurance of salvation:

1.) No teaching (or bad teaching) on key passages regarding a Christian’s absolute, eternal security in Christ.

Rom. 8:35-39 “Who shall separate us from the love of Christ? Shall tribulation, or distress, or persecution, or famine, or nakedness, or peril, or sword? Just as it is written, "For Thy sake we are being put to death all day long; We were considered as sheep to be slaughtered." But in all these things we overwhelmingly conquer through Him who loved us. For I am convinced that neither death, nor life, nor angels, nor principalities, nor things present, nor things to come, nor powers, nor height, nor depth, nor any other created thing, shall be able to separate us from the love of God, which is in Christ Jesus our Lord.”

1 Pet. 5:1 “who according to [God’s] great mercy has caused us to be born again to a living hope through the resurrection of Jesus Christ from the dead, to obtain an inheritance which is imperishable and undefiled and will not fade away, reserved in heaven for you, who are being protected by the power of God through faith for a salvation ready to be revealed in the last time.”

2.) Satanic attack.

3.) Physical pain/difficulties from living in a fallen, broken world.

Sometimes this can cause a person to doubt God’s love for them. This can sometimes be due to a poor teaching on God’s love. It can also be the result of not having a proper understanding of how God chastens/disciplines his children for the purpose of perseverance (Heb. 12). Sometimes we think that all pain is bad, when in reality, it may be the very evidence of God’s love-- though still very painful!

4.) Lack of sharing the Gospel, and being a faithful witness.

This was an experience I (Matt Miller) had when in seminary.

I got to a point when all I did was exist in the bubble of academia.

It was a dark time.

One day I shared the Gospel -- and it felt like fresh air was breathed into me.

And when I looked back on that, I realized that it was simply because I was able to articulate the basic truth of the Gospel. When you are forced to articulate it, and reaffirm what you believe, it has a way of reassuring your soul.

This is part of God’s design.

Some Christians go many years without sharing the Gospel. Well it’s no wonder why they lack assurance. It is part of God’s design in keeping us faithful. As a result, we’ll feel subjectly secure in Christ when we are obedient.

5.) Guilt of sin (perhaps a life-style of sin). God can sometimes pull assurance to draw us back to Him.

1 John 3:24 - ““And the one who keeps His commandments abides in Him, and He in him. And we know by this that He abides in us, by the Spirit whom He has given us.”

So one of the roles of the Spirit is to give us subject assurance, but only as we walk in obedience to the commands of Christ. It is possible for a true christian to walk around in incredible guilt.

When they truly possess the spirit of God, but choose to actively remain in sin, they will feel like a schizophrenic at times.

While trapped in their sin, they still hate it. And so, this can be cause for a very miserable life for the Christian, and it is by design.

As a Christian chooses sin over obedience, they will wonder if they are even saved, and lack that subject feeling of assurance.

It is here where a person must make up their mind what they believe. The true Christain will eventually choose obedience, though it may be a long period of time.

But until that time, they will lack assurance, they will doubt God’s love, and wonder if they are even saved. They will even have thoughts, perhaps, of just giving up on following Christ, altogether.

Again, this is simply due to their own guilt of choosing sin instead of obedience.

But when they eventually come out of that sin and choose obedience, it is amazing how much subjective assurance and joy that a Christian will have, almost immediately.

We would also add, in light of 1 John 3:24 - a true Christian will always lack assurance in times of disobedience.

In fact, it is when a person claims Christ, and knowingly lives in sin, and yet has zero doubt over the salvation, that a pastor should become very concerned.

One of the marks (or evidence) that a person truly possesses the spirit of God, is they begin to lack assurance in times of disobedience.

So one of the worst things a pastor (or fellow Christian) can do, is help minimize that convicting work.

We should let the Spirit’s conviction do it’s work in the life of a sinning believer, and not be quick to minimize it by reminding them that it’s all under the blood, and so they should just have much confidence and ignore their lack of assurance. Rather, lack of assurance is one of God’s tools to keep a true Christian faithfully persevering.

6.) Lack of love for the brethren (1 John is loaded with this theme).

1 John 3:14 - "We know that we have passed out of death into life, because we love the brethren. He who does not love abides in death."

Again, there are so many passages that we could point to in 1 John, but it is no wonder that many who keep the church at arms length wrestle with assurance of their own salvation.

It is simply part of God’s design that the one who loves the brethren will have subjective assurance of their salvation.

If a Christian refuses to faithfully engage in the realm in which the Spirit dwells (i.g., the church), then they should not wonder why they lack assurance from that very same Spirit.

- The Holy Spirit brings about sanctification.

1 Pet. 1:2“according to the foreknowledge of God the Father, by the sanctifying work of the Spirit, that you may obey Jesus Christ and be sprinkled with His blood.”

The Spirit is the primary divine agent Who brings about the process of maturation in our lives. He causes us to be less oriented toward self and more oriented toward Jesus Christ and His will. This is an ongoing, progressive, maturation process that takes place until death.

2 Cor. 3:18“But we all, with unveiled face beholding as in a mirror the glory of the Lord, are being transformed into the same image from glory to glory, this comes from the Lord (YHWH), Who is the Spirit.”

There is also a human agent in sanctification (synergistic process). This comes about through faith, obedience, community, prayer, etc.

- The Holy Spirit is active in missional endeavors.

Acts 1:8“But you shall receive power when the Holy Spirit has come upon you; and you shall be My witnesses both in Jerusalem, and in all Judea and Samaria, and even to the remotest part of the earth."

So the Holy Spirit is active in evangelism, and the pursuit of  missions.

First, the Holy Spirit gives us a desire, and will often prompt us in our missional endeavors. The Holy Spirit will also guide us in our actions.

A helpful passage to see this is Acts 16:6-15:

“And they passed through the Phrygian and Galatian region, having been forbidden by the Holy Spirit to speak the word in Asia; and when they had come to Mysia, they were trying to go into Bithynia, and the Spirit of Jesus did not permit them; and passing by Mysia, they came down to Troas. And a vision appeared to Paul in the night: a certain man of Macedonia was standing and appealing to him, and saying, "Come over to Macedonia and help us. And when he had seen the vision, immediately we sought to go into Macedonia, concluding that God had called us to preach the gospel to them. Therefore putting out to sea from Troas, we ran a straight course to Samothrace, and on the day following to Neapolis; and from there to Philippi, which is a leading city of the district of Macedonia, a Roman colony; and we were staying in this city for some days. And on the Sabbath day we went outside the gate to a riverside, where we were supposing that there would be a place of prayer; and we sat down and began speaking to the women who had assembled. And a certain woman named Lydia, from the city of Thyatira, a seller of purple fabrics, a worshiper of God, was listening; and the Lord opened her heart to respond to the things spoken by Paul. And when she and her household had been baptized, she urged us, saying, "If you have judged me to be faithful to the Lord, come into my house and stay." And she prevailed upon us.”

So, here, Paul and Timothy, joined by Luke, are forbidden to speak the Gospel in certain places. Now how this worked itself out, the Scriptures do not say.

But the Spirit essentially says, “Not here, not now.”

Instead, the Spirit evidently desired Lydia to be brought to salvation. And so, these missionaries of the Gospel traveled 400 miles before they were able to see a convert.

And is from this work that the church at Philippi was then born.

Personal Example: our MKE church plant – We were prevented from going into Illinois, and yet God made things work very quickly in Southern Milwaukee—

Why? He has elect living in Southern Milwaukee that He desires us to reach and grow into maturity.

- The Holy Spirit helps us to pray.

Rom. 8:27-28 “And in the same way the Spirit also helps our weakness; for we do not know how to pray as we should, but the Spirit Himself intercedes for us with groanings too deep for words; and He who searches the hearts knows what the mind of the Spirit is, because He intercedes for the saints according to the will of God.”

We are weak, particularly in our praying, and the Spirit helps us in this.

We sometimes do not know what, how, when, or why to pray. This is written for the purpose of comfort, especially when a Christian is in the midst of suffering.

The Father always hears the intercession of the Spirit, Who is perfectly praying on our behalf, according to the will of God.

- The Holy Spirit of God and the Word of God.

1 Cor. 2:14-16 “But a natural man does not accept the things of the Spirit of God; for they are foolishness to him, and he cannot understand them, because they are spiritually appraised. But he who is spiritual appraises all things, yet he himself is appraised by no man. For who has known the mind of the Lord, that he should instruct Him? But we have the mind of Christ.”

The Spirit was responsible for giving the Word, but is also responsible for illuminating the Word.

Reformation categories:

Notitia - understanding certain facts.

Assensus - agreeing (or assenting) to the fact that those facts are true.

Fiducia - The Spirit can work in the previous two, but this category is the sole work of the Spirit. This is where a person develops a love/hope in those facts. There is a genuine trust in them.

- The Holy Spirit gives guidance.

Rom. 8:1-9 “There is therefore now no condemnation for those who are in Christ Jesus. For the law of the Spirit of life in Christ Jesus has set you free from the law of sin and of death. For what the Law could not do, weak as it was through the flesh, God did: sending His own Son in the likeness of sinful flesh and as an offering for sin, He condemned sin in the flesh, in order that the requirement of the Law might be fulfilled in us, who do not walk according to the flesh, but according to the Spirit. For those who are according to the flesh set their minds on the things of the flesh, but those who are according to the Spirit, the things of the Spirit. For the mind set on the flesh is death, but the mind set on the Spirit is life and peace, because the mind set on the flesh is hostile toward God; for it does not subject itself to the law of God, for it is not even able to do so; and those who are in the flesh cannot please God. However, you are not in the flesh but in the Spirit, if indeed the Spirit of God dwells in you. But if anyone does not have the Spirit of Christ, he does not belong to Him.”

Gal. 5:16-25 “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. But if you are led by the Spirit, you are not under the Law. Now the deeds of the flesh are evident, which are: immorality, impurity, sensuality, idolatry, sorcery, enmities, strife, jealousy, outbursts of anger, disputes, dissensions, factions, envying, drunkenness, carousing, and things like these, of which I forewarn you just as I have forewarned you that those who practice such things shall not inherit the kingdom of God. But the fruit of the Spirit is love, joy, peace, patience, kindness, goodness, faithfulness, gentleness, self-control; against such things there is no law. Now those who belong to Christ Jesus have crucified the flesh with its passions and desires. If we live by the Spirit, let us also walk by the Spirit.”

- The Holy Spirit is involved in church matters (a few categories).


The Spirit sets and establishes leaders in the Church of Jesus Christ.

Acts 20:28 - "Be on guard for yourselves and for all the flock, among which the Holy Spirit has made you overseers, to shepherd the church of God which He purchased with His own blood.”

Acts 13:2 “And while they were ministering to the Lord and fasting, the Holy Spirit said, ‘Set apart for Me Barnabas and Saul for the work to which I have called them.’ Then, when they had fasted and prayed and laid their hands on them, they sent them away. So, being sent out by the Holy Spirit, they went down to Seleucia and from there they sailed to Cyprus.”

This is a narrative text, so it’s explaining what happened, historically. Narrative is generally described from the author’s viewpoint. It’s not intended to function propositionally. As such, this is why we can say that an elder in our church has been established by the Holy Spirit. 

As we recognize certain qualities and giftings; and as they sit, learn, and are examined by the elders, when the elders come to a conclusion that a certain man should be formally established as an elder, we can say, then, that the Spirit has told us to set apart a qualified man for eldership. This is the Spirit’s leading of the local church. It’s always seen in hindsight.

This is also why an unbiblical opposition to leadership is not good. You are opposing the work of the Spirit. And that is not good, especially for your own soul (e.g., Heb. 13:17).


Now, we did a whole episode on unity, so check it out for a much fuller and complete version of this, but it’s interesting to note that 15 of the “sins of the flesh” involve matters related to disunity.

Paul exhorts in Eph. 4:3 that the Church is called to maintain a “unity of the Spirit.”

Eph. 4:1-3 “I, therefore, the prisoner of the Lord, entreat you to walk in a manner worthy of the calling with which you have been called, with all humility and gentleness, with patience, showing forbearance to one another in love, being diligent to preserve the unity of the Spirit in the bond of peace. There is one body and one Spirit, just as also you were called in one hope of your calling; one Lord, one faith, one baptism, one God and Father of all who is over all and through all and in all.”

We are not called to attain (i.e., create or start) a unity of the Spirit, but commanded to maintain the unity of the Spirit. Jesus prayed in Jn. 17 (The High Priestly prayer), a petition on behalf of the Universal Church.

His prayer would be that the Father would make them [the Church] one, just as He [Jesus] and the Father are one. The fulfillment of this prayer would be achieved via the Holy Spirit at Pentecost in Acts 2. We are all one in Jesus Christ by means of His Spirit (This is abundantly clear in Eph. 2:18).

"For through Him [Christ] we both have our access in one Spirit [lit. “by one Spirit”] to the Father.”

This is sovereign work of the Spirit, achieved through the petition of Christ for His Bride (which again, happened in that High Priestly prayer of John 17).

And this is why disunity is evil. You actively oppose the active work of the Trinity (The Father grants the request of the Son, through the uniting work of the Spirit).

Hence, the reason for Paul’s warning in 1Cor. 3:16-17:

1 Cor. 3:16-17 “Do you not know that you are a temple of God, and that the Spirit of God dwells in you? If any man destroys the temple of God, God will destroy him, for the temple of God is holy, and that is what you are.”

Now a “Unity of the Spirit” is not a “unity of the Faith.” 

And this is critical to keep in mind.

In fact, this is the reason so many are busy chasing things in the name of unity, that have nothing to do with the command to “maintain the unity of the Spirit.”

Eph. 4:11-13 “And He gave some as apostles, and some as prophets, and some as evangelists, and some as pastors and teachers, for the equipping of the saints for the work of service, to the building up of the body of Christ; until we all attain to the unity of the faith, and of the knowledge of the Son of God, to a mature man, to the measure of the stature which belongs to the fullness of Christ.”

Notice, the key word “until.” This implies we do not yet have a “unity of the Faith.”

“The Faith” is a technical phrase in reference to the body of Doctrine—the truth of all things.And it’s connected to the phrase “knowledge of the Son of God,” meaning all things concerning the Son.

And, then, notice when the Church will have a “unity of the Faith” – at the fullness of Christ. So this implication is the church will never agree on all matters related to doctrine.

In fact, this is why denominations can be a good thing. Provided it doesn’t concern a heretical issue, this is also why we’ll encourage people to look for a different church at times. We want them to be able to worship in a greater “unity of the Faith.”

In fact, this actually helps maintain a “Unity of the Spirit.”


There is much more we could say, but this is a decent survey. There is a lot that the Spirit does within the church, and it is a gift. We should never forget that this is God’s church, and He cares for it more than we do. He is always at work in ways we do not know, and a primary way is through His Spirit; who is very active and very present, accomplishing everything the Son intends.


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