Four Ways God’s Spirit Speaks to Our Spirit (Part One)

This is the 3rd of a four-part series about the Holy Spirit. You can see part 1 and part 2 here.

These are working sections from a book manuscript I just completed for Zondervan. We’re in the editing process right now, so your thoughts are welcome.

When I was a junior in high school, I once took an “unauthorized” road trip on a Saturday evening to a ski resort several hours away. My friends and I raced home early Sunday morning to try in an attempt to get to church on time so no one would be the wiser about our absence. One friend drove, and the rest of us slept in the car. Then that other friend decided to join us. The car, set on cruise control at 62 miles per hour, barreled off the side of the road into a 20-foot ravine, landing upside down. How any of us survived is miraculous. The crash mangled the car, crushing it in places. Every one of us walked out of the wreck without a scratch.

Just moments before the wreck, I had woken up and shifted from the left back seat to the right. Where my head had previously been, just a few minutes before the crash, was completely crushed; the roof over my new seat remained untouched. And here’s the strangest detail of the story: as we drifted off the road toward the ravine, we hit a discarded mattress lying on the roadside that threw us into a tailspin, which slowed our speed dramatically before we toppled into the ravine. Without that mattress, we would have rocketed into the ravine at more than 60 miles per hour, which surely would have killed us all. I have no idea why a mattress lay on the side the road. What are the odds?

Of course, after we got home I had to tell my parents what happened. As I related the details, my mom asked me what time this had all gone down. I told her, “5:21”, because when I had been jolted awake by the car landing upside down, the digits on the clock were the first thing I saw, though they looked like “12:5” being upside down! She told me that she had awakened at 5:00 that morning with an inexplicable urge to pray for me. She prayed for me for about 30 minutes—for God to work in my life, to get my attention, to protect me, and to perfect his will in my life. At 5:30 she went back to sleep. Boy, did God answer that prayer.

I tell you that story for two reasons:

A. To demonstrate how God often moves our spirits to pray for others.

B. To request that if God ever wakes you up at 5 am with a strong desire to pray for me that you do so.

Christ, the church’s “head,” does his work through his body, the church, by placing into our hearts words of warning and encouragement, burdens and holy ambitions that he has for his people. Our bodies may provide the agency for his work, but he is the head. As members of his body, he accomplishes his purposes through us.

But It Makes Me Nervous

I admit that discussing how we can “hear from God” makes me nervous. How do you know the difference between a genuine movement of the Holy Spirit in your heart and, say… indigestion? (And I’m not trying to be funny.) Between a special burden and excess emotion that comes from too little sleep?

Let me make clear that what I’m going to share with you in these pages is not “the final word” on these matters. I’ve tried for several years to glean everything I can on this from Scripture, to reflect honestly on my own experiences, and to listen cautiously to other Spirit-filled believers recount how God has moved in their lives. As we discussed earlier, being led by the Spirit is not an exact science. We shouldn’t think of this process like a formula, and we should always approach this subject with an extreme amount of humility—as befits a living relationship. And we should remain very cautious about declaring with absolute certainty that God has put something on our hearts unless it has a chapter and verse attached to it. I believe it is clear that God does move and speak in our spirits, but we must hold our certainty about his leadership with a little tenuousness, open to godly counsel, always subject to Scripture.

For example, let me tell you a story about a time I (evidently) got it wrong. After my wife and I had three kids, we sought God about whether to have more. At three kids, I felt like my quiver was full. At no point in the week did I feel like I needed more to do or another mouth to feed. But we also knew that rearing godly children is among the greatest ministries you can have (Ps. 127:1–4), so we thought, “Well, why not have one more—for Jesus?” God had also touched our hearts for regarding adoption, and so we prayed about whether we should do that, too. We set aside a day—April 28, 2009—for a time of prayer and fasting.

At the end of that day, we both felt that God was leading us to pursue an international adoption. But when Veronica woke up the next morning, however, she felt sick… and yep, you guessed it: she was pregnant. I don’t think I’ve ever had a prayer answered that quickly, that definitively. While we were seeking God about what to do next, the answer had been (unbeknownst to us) growing inside of Veronica for nearly six weeks.

But what about the “sense” that our next kid was to come through international adoption? Maybe that’s something we are supposed to pursue later, but it was not what God had for us at the moment. After that experience, we contributed personally to several other families in our church pursuing adoption. The “sense” that we were to do it in 2009 was overruled, however, by, well, God’s definitive answer in our circumstances.

That’s one of the reasons I say you should always hold what you think God is “saying” to you loosely. God simply did not outline for us in Scripture a definitive way to know (with absolutely certainty) that he is moving in our spirits about something. I’ve searched every passage in the Bible related to that topic, looking for the definitive answer. There is none. So when it comes to areas of life not spelled out by Scripture, while we can strongly suspect something to be God’s will, and act boldly in pursuit of it, we should always stop short of the absolute certainty we give to Scripture.

With that understood, let me give you four ways I have experienced God speaking in my spirit which I see consistent with Scripture:

1. Particular Burdens As I Pray

The prophet Habakkuk said,

“I will take my stand at my watchpost and station myself on the tower, and look out to see what he will say to me.” (Habakkuk 2:1)

Prayer is supposed to be a two-way conversation. Prayer is not just informing God of things going on in which we could use his help (he already knows about them anyway). In prayer, we also hear from God about what he wants to do about these things and by faith lay hold of his provision for those things. I’ve heard it said that prayer works like a laser beam. You create a laser by stacking light waves on top of one another, channeling all the photons in the same direction. A handful of photons going in different directions yield only a soft, incandescent glow, but when you stack and concentrate the light waves, they release a power that can cut through steel.

In prayer, you stack the “wave” of your faith to the “wave” of the Spirit’s prompting, releasing the laser beam of God’s power. If our prayer request first comes from heaven, it will certainly obtain heaven’s help. Prayers that start in heaven get heard by heaven.

Paul promised the Spirit would help us as we prayed, and often talked himself about praying “in the Spirit.” What exactly does prayer “in the Spirit” mean? John Piper says,

It seems clear to me that speaking “in the Spirit” means speaking under the guidance of the Spirit, or energized and helped by the Spirit. That’s why no one can say “Jesus be accursed” when speaking “in the Spirit.” And no one can say, “Jesus is Lord” (and mean it) unless he is speaking “in the Spirit.” So I take it that praying “in the Spirit” means praying under the guidance and with the help and energy of the Spirit. The Spirit is shaping our prayers and helping us pray.[1]

What does this experience “feel” like? Quite often the Spirit does it in the background, acquainting us with situations he wants to pray about. We may not have a special “feeling” that we need to pray, but God’s sovereignty has arranged our circumstances so that we pray about the things he wants us to prayer about. But sometimes as I pray God seems to press in on my heart a particular burden, or verse of Scripture, about the person or situation for which I am praying. I don’t automatically assume that whatever pops into my mind as I pray is the voice of God, but I will often jot down the verse or thought, and ask the Spirit to confirm whether he’s put that in my heart by bringing it up to me again. Sometimes I will share that verse or burden with the person, and on numerous occasions they have told me it was as if the Holy Spirit was speaking directly to them through the verse or promise that I shared.

I have encouraged our church to develop the habit of “listening prayer.” Ask God to bring to your mind verses and special burdens as you pray and listen for how he might do so. Prayer ought to be less a presentation of a catalogue of needs and more an experience of communion with a living Father.

I have a written out prayer list for each of my four kids. I try to remain very sensitive to verses of Scripture the Spirit drops into my heart for each of them when I pray. Not long ago God had given me a specific verse to pray over my oldest daughter about the fear of God and the praise of men. One afternoon I told her what God had given me for her. While she will often listen to my counsel, these words seem to resonate in her in an unusual way. God used the words of this verse, which he had given to me for her, to speak directly into an area of her life.

The more Scripture you know, the more illumination the Holy Spirit can give to you regarding his heart for various people. God has never brought to my mind a Scripture I did not already know. I know some who claim he has done that for them, but I think the normal way he works is to bring to mind the Scriptures we have hidden in our hearts. Memorizing Scripture is like stocking myself with ammunition for the Spirit to fire as I pray—promises I can claim, warnings I can heed. The Bible contains over 3000 promises. I want to know all of them. God did not give us the Bible simply to read through, but to pray through.

As we’ve learned over and over throughout this book, being led by the Spirit of God in prayer will be proportionate on your knowledge of the Word of God. Remember, the word is his primary weapon. Paul called the Word of God “the sword of the Spirit!” (Eph 6:17)

Charles Spurgeon described his experience praying in the Spirit this way:

He [the Spirit] guides us in prayer; thus, he helps our infirmities. But the blessed Spirit does more than this; he will often direct the mind to the special subject of prayer. He dwells within us as our Counselor and points out to us what it is we should seek at the hands of God. We do not know why it is so, but we sometimes find our minds carried as by a strong undercurrent into a particular line of prayer for some definite purpose. It is not merely that our judgment leads us in that direction, though usually the Spirit of God acts upon us by enlightening our judgment, but we often feel an unaccountable and irresistible desire rising within our hearts.

He will guide you both negatively and positively. Negatively, he will forbid you to pray for certain things, just as Paul tried “to go into Bithynia: but the Spirit suffered [him] not” (Acts 16:7). On the other hand, he will cause you to hear a cry within your soul that will guide your petitions, even as he made Paul to hear the cry from Macedonia, saying, “Come over into Macedonia, and help us” (v. 9).[2]

2. Special Insights Into People and Situations

Recently I was praying for a couple in my small group when I sensed God impressing upon me that he had something really special for their son, who was at the time 10 years old. They are a newly saved couple, and (unbeknownst to me) worry about the bad habits they may have sown into him for the first 10 years of his life. But as I prayed, I felt a certainty that God’s hand was upon him, that God was working in his life, and that God wanted me to communicate that to them—that they should follow him closely and trust him (1 Chronicles 28:9–10). I told them that I believed God was telling them that he had brought them to salvation just when he wanted to, and that he had already provided for their children. I told them that the future of their family was in his merciful hands. The relief on their face told me everything.

I don’t sense things like this every time I pray, but I sensed it this time, and so I told them what was in my spirit. I am anxious to see what God does with it. Here’s why.

When I was four years old, a pastor told my parents something very similar about me. He said simply, “God has something special for this one.” At four years old, I was not demonstrating any qualities that would make you think God had set me apart for anything. In fact, for many years after that I walked away from God—and hard. Yet this pastor perceived the Spirit’s purpose and called it out. My parents prayed this word back to God during the time I wandered, and rejoiced in it later when he brought me back to himself and called me into his service.

Praying with the help of the Spirit means asking God how to pray more specifically about certain situations and to instruct us in what he wants us to say or do. Throughout history Christian believers have reported God moving in their hearts this way:

Once, during a sermon, Charles Spurgeon pointed to a young man in the balcony he did not know and said, “Young man, the gloves in your pocket are not paid for.”[3]

R. C. Sproul said that early on in his ministry he had this sudden thought: “Go throughout the world and preach the Gospel to every living creature…. Take Vesta [his future wife] with you.”[4]

Cotton Mather, an early American Puritan theologian with heavy influence on Jonathan Edwards, said that God sometimes gives a “special” faith to believers during prayer that assures them of what he’s going to do: In addition to ‘general’ faith in Christ, there is a particular faith that is granted to believers now and then, under the energy of some superior cause, a strong Impression made upon his mind, which dissolves him in a flood of tears, and assures him, “You shall have the petition which you desire of God.” The impression is born upon his mind, with as clear a light, and as full a force, as if it were from heaven angelically… these are instances of the prophetic spirit upon believers.[5]

Sometimes God gives us foreknowledge about situations he wants us to get prepared for. The Holy Spirit told the Apostle Paul, for example, that danger awaited the ship he sailed on, which helped prepare Paul to minister to the passengers when it happened and convinced those on the ship to listen to him. The prophet Agabus warned that a famine would affect the whole Roman world (Acts 11:28). Very similar things happened to Martin Luther and Presbyterian theologian John Flavel.[6]

These are instances of the Holy Spirit moving in the spirits of his children, and time and experience confirmed that the “impression” really was from God. (And, by the way, in case you wonder why I am using a lot of older theologians you may not have heard of as my examples, I am trying to show you that the experience of God speaking in the spirit is not something invented by modern day TV evangelists, but has been the experience of believers of all traditions throughout church history.)

Jesus told his disciples that if they had faith they could move mountains. Does that mean that I can go up to any old mountain any time I want and say, “Hmm… I don’t feel like going over you. Get out of my way!” No. The Spirit fills us at certain times with faith for certain mountains. Adding the wave of your faith to the wave of his will releases the laser of his power.


[1] John Piper, “Praying in the Closet and in the Spirit,” Message on Matthew 6:1–5,

[2] Spurgeon on the Holy Spirit (New Kensington, PA: Whitaker House, 2000), 102–3

[3] Ernest W. Bacon, Spurgeon: Heir of the Puritans (Grand Rapids: Eerdmans, 1968) 156.

[4] Ligonier Ministries, “Striking a Chord in the Heart of the Believer,” Table Talk 14 no. 11 (Nov., 1990) 13.

[5] Cotton Mather, Parentator: Memoirs of Remarkables in the Life and the Death of the Ever-Memorable Dr. Increase Mather (Boston: B. Green, 1724) 189-91. Cited by Poythress. I paraphrased Mather’s words slightly because they are written in very old English, but I have preserved accurately his meaning. To note, Mather also issues several cautions and warns of counterfeits on pp. 191–96.

[6] Vern Poythress, “Modern Spiritual Gifts as Analogous to Apostolic Gifts: Affirming Extraordinary Works of the Spirit within Cessationist Theology,” The Journal of the Evangelical Theological Society 43 39/1 (1996): fn. 25.

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