Holy Spirit teaches us that we human beings are three-part beings just as God is a three-part being. He is God the Father, God the Son, and God the Holy Spirit. We learn from the letter the Apostle Paul wrote to the church at Thessalonica that we are spirit, soul, and body. Another way to say this is that we are a spirit, we have a soul, and we live in a body. This Bible study aims to explore our three-part nature and how we can grow in our faith in Jesus Christ based on this knowledge.
1 Thessalonians 5:23 NIV
May God himself, the God of peace, sanctify you through and through. May your whole spirit, soul and body be kept blameless at the coming of our Lord Jesus Christ.
Notice that the most important part of us, our spirit, is listed here first. Then our soul is listed and lastly, the body. There are many, many scriptures that explain how to assess and manage each part of our being. This will not be an exhaustive study, but it will give some basics and a place to start.
The spirit of a person is that part of us that is made in the likeness and image of God. Jesus spoke this about God’s nature.
John 4:24 AMPC
God is a Spirit (a spiritual Being) and those who worship Him must worship Him in spirit and in truth (reality).
Our spirit is the part of us that is re-created or born again when we hear the gospel and trust in Jesus as our Lord and Savior. Our soul is composed of our mind, our will, and our emotions. It can be restored or healed. It can be repaired or renewed. Damaged or diseased parts of our soul can be subjected to the Great Physician’s remedies. Our body is the part of us that is material and allows us to live on this earth. When our body dies, we can no longer be a part of the natural earth’s system. As we will see in this Bible study, the body must be disciplined and controlled. It will be necessary to deal with it by faith and the Word of God.
When Adam and Eve were created, spiritually, they were alive to God. When they rebelled against God, obeyed the serpent, and sinned, they died spiritually. God warned Adam not to eat from the Tree of the Knowledge of Good and Evil. He told him that in the day he ate of that tree, he would “die.”
Genesis 2:15-17 NIV
15 The Lord God took the man and put him in the Garden of Eden to work it and take care of it. 16 And the Lord God commanded the man, “You are free to eat from any tree in the garden; 17 but you must not eat from the tree of the knowledge of good and evil, for when you eat from it you will certainly die.”
In Genesis chapter 3, we learn of Adam and Eve’s rebellion. However, they did not die physically. They died spiritually. Their human spirits that were alive to God died. Their bodies and souls lived on.
Remedy for the Spirit
God’s remedy for a dead spirit is the new birth. Paul describes the new birth in 2 Corinthians 5.
2 Corinthians 5:17-18 AMPC
17 Therefore if any person is [ingrafted] in Christ (the Messiah) he is a new creation (a new creature altogether); the old [previous moral and spiritual condition] has passed away. Behold, the fresh and new has come! 18 But all things are from God, who through Jesus Christ reconciled us to Himself [received us into favor, brought us into harmony with Himself] and gave to us the ministry of reconciliation [that by word and deed we might aim to bring others into harmony with Him].
Jesus describes the new birth in the Gospel of John, chapter 3, in a discussion with a religious leader named Nicodemus.
John 3:3-6 AMPC
3 Jesus answered him, I assure you, most solemnly I tell you, that unless a person is born again (anew, from above), he cannot ever see (know, be acquainted with, and experience) the kingdom of God. 4 Nicodemus said to Him, How can a man be born when he is old? Can he enter his mother’s womb again and be born? 5 Jesus answered, I assure you, most solemnly I tell you, unless a man is born of water and [even] the Spirit, he cannot [ever] enter the kingdom of God. 6 What is born of [from] the flesh is flesh [of the physical is physical]; and what is born of the Spirit is spirit.
In this passage, Jesus makes a distinction between spirit and flesh. We are born of flesh first. Then, by an act of faith through grace, we are born again in our spirits. Jesus says, basically, “that which is born of flesh is flesh and that which is born by Holy Spirit is spirit.” There is a vast gulf between our spirits and our bodies. They can be connected by the soul; however, the soul must be restored to be effective in creating a useful connection between body and spirit. The Apostle Peter has beautiful things to say about the new birth.
1 Peter 1:3-4, 23 NASB
3 Blessed be the God and Father of our Lord Jesus Christ, who according to His great mercy has caused us to be born again to a living hope through the resurrection of Jesus Christ from the dead, 4 to obtain an inheritance which is imperishable and undefiled and will not fade away, reserved in heaven for you
23 for you have been born again not of seed which is perishable but imperishable, that is, through the living and enduring word of God
The King James version of the Bible uses the words “corruptible” and “incorruptible” in place of “perishable” and “imperishable.” “Imperishable” speaks of the longevity and vitality of the seed. “Incorruptible” speaks of the quality, virtue, and excellence of the seed. We are born-again by the incorruptible and imperishable Word of God.
The Apostle Paul also describes the new birth in his letter to the church of Ephesus.
Ephesians 2:1-7 GNT
1 In the past you were spiritually dead because of your disobedience and sins. 2 At that time you followed the world’s evil way; you obeyed the ruler of the spiritual powers in space, the spirit who now controls the people who disobey God. 3 Actually all of us were like them and lived according to our natural desires, doing whatever suited the wishes of our own bodies and minds. In our natural condition we, like everyone else, were destined to suffer God’s anger.
4 But God’s mercy is so abundant, and his love for us is so great, 5 that while we were spiritually dead in our disobedience, he brought us to life with Christ. It is by God’s grace that you have been saved. 6 In our union with Christ Jesus he raised us up with him to rule with him in the heavenly world. 7 He did this to demonstrate for all time to come the extraordinary greatness of his grace in the love he showed us in Christ Jesus
Notice in verses 1 and 5 above that we are spiritually dead and the raising up and ruling with Christ is spiritual raising and ruling.
The human eye cannot see the human spirit. We know what our born-again spirit looks like by looking at descriptions provided by the New Testament scriptures. This new creation that Paul described in 2 Corinthians 5 can only be observed in the Word of God. Consider Ephesians 1, verse 3.
Ephesians 1:3 NASB
Blessed be the God and Father of our Lord Jesus Christ, who has blessed us with every spiritual blessing in the heavenly places in Christ,
Your born-again spirit is blessed with every spiritual blessing that God has. Your soul might not look like it is blessed with every spiritual blessing in heavenly places and your body might not look like it has been blessed with every spiritual blessing in heavenly places, but that is exactly what your new creation spirit looks like. Your soul (mind, will, and emotions) is not born again. There will often be immediate healing of emotions or other components of your soul, but ultimately your soul will be a faith project that you will work on throughout your life. Your body does not get re-created at the new birth either. It is flesh and it is going to have to be subjected to discipline often throughout your life.
Later in chapter one of Ephesians, Paul makes this statement:
Ephesians 1:13, 14 ESV
13 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, 14 who is the guarantee of our inheritance until we acquire possession of it, to the praise of his glory.
The word “sealed” is sphragizo (Strong’s Concordance G4972) in the Greek. This word has meaning which include:
-to set a seal upon or to mark with a seal, to impress with a seal or a stamp, to authenticate or place beyond doubt-
Historically, documents or missives were sealed when melted wax was applied, and a signet ring was stamped into the wax to assure the receiver that it was genuine. Today our notary public will stamp a document to authenticate it. A seal is a way of guaranteeing that the thing to which the seal is affixed is valid and true. The word “seal” can also be used as a “closing up against contamination.” The new birth is a holy work of power performed by Holy Spirit in response to a step of faith in the Gospel. With this work of power comes a guarantee of an inheritance. Paul also told the Corinthians the following about the new birth and our inheritance:
1 Corinthians 6:17 NASB
But the one who joins himself to the Lord is one spirit with Him.
When we join ourselves to Jesus by grace through faith, Holy Spirit joins our spirit to Jesus’ Spirit. Our born-again human spirit looks like Jesus. It is complete in Christ (Colossians 2:10). At our new birth, Holy Spirit creates a new, alive-to-God spirit that is joined to and enlivened by Jesus. To know what you look like spiritually, you look at Jesus. Look to the places in the New Testament where it says “in Christ…” or “in Him…” and what follows will be the description of your new-creation spirit. Working these characteristics out in the soul and flesh can be done but will probably take a little more time.
Remedy for the Soul
The human soul is the seat of all emotion, will, intellect, and psychological processes. Very few people get very far in life without sustaining damage to their souls. Some people sustain massive damage to their souls before they are even old enough to process their surroundings and their relationships. Thank God, thank God, He has a remedy for broken, traumatized, abused souls.
Psalm 23 NASB
1 The Lord is my shepherd, I shall not want. 2 He makes me lie down in green pastures; He leads me beside quiet waters. 3 He restores my soul; He guides me in the paths of righteousness, For His name’s sake.
In King David’s famous twenty third Psalm, a declaration is made that God restores our souls. Like the new birth, restoration of our souls is an act of grace through faith. We have to reach out in faith and ask God to begin His work of restoring, repairing, and rebuilding our minds, wills, and emotions. God the Father is always only good. He hears and answers these prayers. Unlike the new birth, which is an instantaneous work of Holy Spirit’s power, soul-restoration usually takes more time. For some, certain aspects of soul-brokenness are restored at the new birth. However, many areas of our minds, wills, and emotions will take time and faith to repair the damage that has been done.
Faith begins where the will of God is clearly known. Faith for restoration of souls begins with learning and meditating on scriptures that announce God’s desire and willingness to provide the soul remedy. Sustaining and maintaining a restored soul also depends on learning and meditating God’s Word.
2 Corinthians 1:3, 4 AMPC
3 Blessed be the God and Father of our Lord Jesus Christ, the Father of sympathy (pity and mercy) and the God [Who is the Source] of every comfort (consolation and encouragement), 4 Who comforts (consoles and encourages) us in every trouble (calamity and affliction), so that we may also be able to comfort (console and encourage) those who are in any kind of trouble or distress, with the comfort (consolation and encouragement) with which we ourselves are comforted (consoled and encouraged) by God.
Our kind and compassionate Heavenly Father provides deep comfort for us. He has great sympathy and pity for the people walking around this planet with severely broken souls. He can provide a supernatural, miraculous “download” of soul healing and restoration instantly or He can send Hisord to heal our souls over a period of time
Psalm 107:20 AMPC
He sends forth His word and heals them and rescues them from the pit and destruction.
Proverbs 4:20-23 AMPC
20 My son, attend to my words; consent and submit to my sayings. 21 Let them not depart from your sight; keep them in the center of your heart. 22 For they are life to those who find them, healing, and health to all their flesh. 23 Keep and guard your heart with all vigilance and above all that you guard, for out of it flow the springs of life.
Reading, studying, meditating, pondering, declaring, or journaling the Holy Scriptures appropriates and activates this medicine to the soul. The Word has power in itself to restore souls and renew minds. Our minds are the components of our souls that can be particularly stubborn and resistant to restoration and repair. If we feed on the world’s system of information and adhere to its values, making progress in the restoration of the soul will be impossible.
Romans 12:2 AMPC
Do not be conformed to this world (this age), [fashioned after and adapted to its external, superficial customs], but be transformed (changed) by the [entire] renewal of your mind [by its new ideals and its new attitude], so that you may prove [for yourselves] what is the good and acceptable and perfect will of God, even the thing which is good and acceptable and perfect [in His sight for you].
The New Living Translation says it this way.
Romans 12:2 NLT
Don’t copy the behaviors and customs of this world, but let God transform you into a new person by changing the way you think. Then you will learn to know God’s will you, which is good and pleasing and perfect.
We must begin to think like God thinks for healing and restoration to occur. We must reject worldly wisdom, philosophies, attitudes, and opinions. The world’s thinking is literally authored and inspired by Lucifer himself. The world’s wisdom, philosophies, attitudes, and opinions are poisonous to our minds, wills and emotions and will keep our souls in a state of torment. Practically, what we have to do is shut down and turn off all sources of information, media, and possibly even relationships that are inspired by the evil one. If you are praying and asking God to restore your soul, Holy Spirit is going to be prompting you to turn things off and shut off certain sources of information. He will be prompting you to read this scripture or study that passage in your Bible. It is important to obey these promptings. Soul-restoration requires obedience to the things Jesus speaks to you.
Isaiah 30:21 AMPC
And your ears will hear a word behind you, saying, This is the way; walk in it, when you turn to the right hand and when you turn to the left.
John 10:3, 4, 27 NASB
3 To him the doorkeeper opens, and the sheep hear his voice, and he calls his own sheep by name and leads them out. 4 When he puts forth all his own, he goes ahead of them, and the sheep follow him because they know his voice….. 27 My sheep hear My voice, and I know them, and they follow Me.
Psalms 32:8 NASB
I will instruct you and teach you in the way which you should go; I will advise you with My eye upon you.
Here is this same verse from Psalms 32 in the New Living Translation and the Message.
Psalm 32:8 NLT
The Lord says, “I will guide you along the best pathway for your life. I will advise you and watch over you.
Psalms 32:8 MSG
Let me give you some good advice; I’m looking you in the eye and giving it to you straight.
Father God wants to heal and restore our souls. But it is important that we listen, pay attention, and obey what we are being told about getting to the place of safety and wholeness. It is very important to keep your soul – your mind, your will, and your emotions – saturated with God’s medicine. The world’s philosophies are poisons and toxins that will keep your soul sick and broken. Perhaps some of the best advice comes from the Apostle James.
James 1:21 AMPC
So get rid of all uncleanness and the rampant outgrowth of wickedness, and in a humble (gentle, modest) spirit receive and welcome the Word which implanted and rooted [in your hearts] contains the power to save your souls.
The Word of God contains power in itself to perform God’s will. Consider these verses from Hebrews, Colossians, and the Gospel of Luke.
Hebrews 4:12 AMPC
For the Word that God speaks is alive and full of power [making it active, operative, energizing, and effective]; it is sharper than any two-edged sword, penetrating to the dividing line of the breath of life (soul) and [the immortal] spirit, and of joints and marrow [of the deepest parts of our nature], exposing and sifting and analyzing and judging the very thoughts and purposes of the heart.
Colossians 1:5, 6 AMPC
Because of the hope [of experiencing what is] laid up (reserved and waiting) for you in heaven. Of this [hope] you heard in the past in the message of the truth of the Gospel, 6 Which has come to you. Indeed, in the whole world [that Gospel] is bearing fruit and still is growing [by its own inherent power], even as it has done among yourselves ever since the day you first heard and came to know and understand the grace of God in truth. [You came to know the grace or undeserved favor of God in reality, deeply and clearly and thoroughly, becoming accurately and intimately acquainted with it.]
Luke 1:37 AMPC
For with God nothing is ever impossible and no word from God shall be without power or impossible of fulfillment.
Notice that the passage in Hebrews says that God’s word is alive and full of power and the passage in Colossians says that the Gospel contains its own inherent power. The verse in Luke quotes and angel speaking to Mary about how she would conceive the God-Man, Jesus Christ. God’s Word initiated the virgin birth of our Savior. It is powerful beyond comprehension.
The path to soul-restoration is straight though the Word of God. Returning to James 1:21 we see that the word of God is able to “save” our souls. The word save, translated from the Greek, is sozo (Strongs’ Concordance G4982). Sozo is a rich word that can be defined in the following way:
-to save, keep safe and sound, to rescue from danger or destruction, to save a suffering one, to make well, heal restore to health, to preserve from danger, to deliver-
The human soul is “sozoed” when God’s Word in planted in the heart and mind. God’s prescription for a healthy soul is His Word.
The Book of Psalms uses the word “soul” almost 300 times in the New American Standard Bible. David and the other psalmists often wrote about the condition of their souls. Many today can I identify with the cries and prayers in the Psalms concerning their souls. Consider the following selected verses.
Psalms 6:4 NASB
Return, Lord, rescue my soul; Save me because of Your mercy.
Psalms 19:7 NASB
The Law of the Lord is perfect, restoring the soul; The testimony of the Lord is sure, making wise the simple.
Psalms 31:7, 8 NASB
7 I will rejoice and be glad in Your faithfulness, Because You have seen my misery; You have known the troubles of my soul, 8 And You have not handed me over to the enemy; You have set my feet in a large place. 9 Be gracious to me, Lord, for I am in distress; My eye is wasted away from grief, my soul and my body too.
Psalms 33:21 NASB
Our soul waits for the Lord; He is our help and our shield.
Psalms 34:22 NASB
The Lord redeems the souls of His servants, And none of those who take refuge in Him will suffer for their guilt.
The Lord redeems the souls of His servants, and none will suffer for their guilt. There is a remedy for a broken soul. It is through prayer and faith in the promises of God.
Remedy for the Flesh
1 Thessalonians 5:23 AMPC
And may the God of peace Himself sanctify you through and through [separate you from profane things, make you pure and wholly consecrated to God]; and may your spirit and soul and body be preserved sound and complete [and found] blameless at the coming of our Lord Jesus Christ (the Messiah).
This passage states that our spirits and souls and bodies can be preserved sound and complete and found blameless at the coming of Jesus. However, there are some cautions regarding the body of flesh we live in. Jesus taught that the flesh and the spirit are distinctly different and that the flesh does not profit.
John 3:6 AMPC
What is born of [from] the flesh is flesh [of the physical is physical]; and what is born of the Spirit is spirit.
John 6:63 AMPC
It is the Spirit Who gives life [He is the Life-giver]; the flesh conveys no benefit whatever [there is no profit in it]. The words (truths) that I have been speaking to you are spirit and life.
Although we need a live body to dwell on this earth, flesh is not beneficial. The Apostle Paul said basically the same thing to the Italian Christians in Rome.
Romans 7:18 NASB
For I know that nothing good dwells in me, that is, in my flesh; for the willing is present in me, but the doing of the good is not.
Romans 8:5-8 NASB
5 For those who are in accord with the flesh set their minds on the things of the flesh, but those who are in accord with the Spirit, the things of the Spirit. 6 For the mind set on the flesh is death, but the mind set on the Spirit is life and peace, 7 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, 8 and those who are in the flesh cannot please God.
These are strong indictments against the flesh. It profits nothing, nothing good dwells in it and it is hostile to God! Paul said this to the brothers and sisters at Corinth.
1 Corinthians 15:50-57 NKJV
50 Now this I say, brethren, that flesh and blood cannot inherit the kingdom of God; nor does corruption inherit incorruption. 51 Behold, I tell you a mystery: We shall not all sleep, but we shall all be changed— 52 in a moment, in the twinkling of an eye, at the last trumpet. For the trumpet will sound, and the dead will be raised incorruptible, and we shall be changed. 53 For this corruptible must put on incorruption, and this mortal must put on immortality. 54 So when this corruptible has put on incorruption, and this mortal has put on immortality, then shall be brought to pass the saying that is written: “Death is swallowed up in victory.” 55 “O Death, where is your sting? O Hades, where is your victory?” 56 The sting of death is sin, and the strength of sin is the law. 57 But thanks be to God, who gives us the victory through our Lord Jesus Christ.
While a fleshly body gives us license or authority to live on the earth, it cannot exist in the glory of heaven. Flesh is corruptible. And the flesh is not born-again. It has to be controlled and disciplined the body to obey the desires of our spirit and renewed soul. The Apostle Paul not only gave us insight into the nature of this flesh, but also what to do about it.
1 Corinthians 9:27 NLT
I discipline my body like an athlete, training it to do what it should. Otherwise, I fear that after preaching to others I myself might be disqualified.
Our physical bodies must be disciplined and trained by faith with patience. As those who are justified by faith, we also live by faith in the natural world (see Habakkuk 2:4, Romans 1:17, Galatians 3:11 and Hebrews 10:38). Managing the physical body, like soul-restoration, requires continual surrender to the Word. It requires saturation in the Word. Remember, there is power in the scriptures to accomplish themselves.
One component of the flesh that requires discipline is appetite. Eating and drinking too much of the wrong things is addressed in the scriptures.
Proverbs 23:1, 2 NASB
1 When you sit down to dine with a ruler, Consider carefully what is before you, 2 And put a knife to your throat If you are a person of great appetite.
The practical application of this verse might be to simply eat half what your fleshly appetite is demanding. Combine that wisdom with the following proclamation from the book of Psalms.
Psalms 37:4 AMPC
Delight yourself also in the Lord, and He will give you the desires and secret petitions of your heart
In prayer, ask God to cause you to want to control your appetite more than you want to indulge your appetite. We are not supposed to be anxious about anything but to pray about everything.
Philippians 4:6 AMPC
Do not fret or have any anxiety about anything, but in every circumstance and in everything, by prayer and petition (definite requests), with thanksgiving, continue to make your wants known to God
“Everything” includes an overactive appetite. Bring this request to God and get your faith involved with your prayer and self-control will begin to manifest. Many of the weaknesses and frailties of the flesh are addressed in scripture. It may be necessary to do some research, but one over-arching scripture verse always applies.
Psalm 138:8 NASB
The Lord will accomplish what concerns me; Your lovingkindness, O Lord, is everlasting; Do not forsake the works of Your hands.
This verse establishes once and for all that God will get involved and help us with anything that worries us, bothers us, tempts us, torments us, or in anyway concerns us. We face nothing alone. We always have the help and support of a kind and loving Father. The help from God might be angels sent to minister to us, Holy Spirit’s specific instruction on an issue, or a fellow saint with a word of knowledge.
Psalm 20:1, 2 AMPC
May the Lord answer you in the day of trouble! May the name of the God of Jacob set you up on high [and defend you]; Send you help from the sanctuary and support, refresh, and strengthen you from Zion;
Help for us from God is unlimited. His creativity in designing this help is unlimited. His power in delivering this help is unlimited. Seek Him in His Word, in prayer, and in worship and your flesh will develop the discipline it needs.
Other verses in scripture that encourage and instruct us concerning the Word of God and its ability to help and change us are found in the books of Joshua and Psalms.
Joshua 1:8 ERV
Always remember what is written in that book of law. Speak about that book and study it day and night. Then you can be sure to obey what is written there. If you do this, you will be wise and successful in everything you do
Psalms 1: 1-3 AMPC
1 Blessed (happy, fortunate, prosperous, and enviable) is the man who walks and lives not in the counsel of the ungodly [following their advice, their plans and purposes], nor stands [submissive and inactive] in the path where sinners walk, nor sits down [to relax and rest] where the scornful [and the mockers] gather. 2 But his delight and desire are in the law of the Lord, and on His law (the precepts, the instructions, the teachings of God) he habitually meditates (ponders and studies) by day and by night. 3 And he shall be like a tree firmly planted [and tended] by the streams of water, ready to bring forth its fruit in its season; its leaf also shall not fade or wither; and everything he does shall prosper [and come to maturity].
Psalm 119: 9-11 TLB
9 How can a young man stay pure? By reading your Word and following its rules. 10 I have tried my best to find you—don’t let me wander off from your instructions. 11 I have thought much about your words and stored them in my heart so that they would hold me back from sin.
The God that fashioned and formed each one of us created us to be a spiritual being, to have a soul, and to live in a body. Each day we should be aware of our three-part nature. We should recognize and live from the perfection, the beauty, and the incorruptibility of our born-again spirits. We should be engaged in soul restoration and healing. And we should, by faith and the Word, be living in a physical body that is learning discipline and obedience.
As you study and pray over these verses, consider the following worship songs.
Spirit Lead Me – Michael Ketterer
Holy Water – We the Kingdon