Healing our subconscious (emotional) minds

To follow Jesus, we are called to deny ourselves and put off our old selves. What we may not realise is that the old self is very much ruled by our subconscious minds, which are in turn, influenced by our feelings and reflexes. We can mentally tell ourselves what we ought to do but don’t always follow through because our emotions led us astray. It is little wonder that the Bible says that our desires are “deceitful”. The key to turning from the old self and being wonderfully renewed to follow Jesus is to set our minds on the Holy Spirit and live according to His direction. That is where we will find everlasting life and peace. God is good, generous, faithful and kind to all those who seek Him.

(See Chinese versions: 简体中文 > 医治我们潜意识（情感）的头脑 | 繁體中文 > 醫治我們潛意識（情感）的頭腦)

Ephesians 4:22-24 ESV  to put off your old self, which belongs to your former manner of life and is corrupt through deceitful desires, and to be renewed in the spirit of your minds, and to put on the new self, created after the likeness of God in true righteousness and holiness.

Romans 8:5-7 ESV For those who live according to the flesh set their minds on the things of the flesh, but those who live according to the Spirit set their minds on the things of the Spirit. For to set the mind on the flesh is death, but to set the mind on the Spirit is life and peace. For the mind that is set on the flesh is hostile to God, for it does not submit to God’s law; indeed, it cannot.



As followers of Jesus Christ, we are called to rule over our deceitful desires so we do not sin. Yet anyone who has tried will tell you that it is virtually impossible to do so on our own human strength. As much as we like to think of ourselves as rational beings, it is ultimately our subconscious (emotional) thoughts that drive our choices – and this world is filled with people and issues that set off our emotions in undesired directions. Most of us don’t really understand why we do the things we do, because we are not really aware of all our underlying emotions.

James 1:14-15 ESV  But each person is tempted when he is lured and enticed by his own desire. Then desire when it has conceived gives birth to sin, and sin when it is fully grown brings forth death.

As a consequence, we grieve the Holy Spirit when we give in to emotions such as hostility, jealousy, anger, envy, fear and bitterness. The Bible warns us that we will not inherit the kingdom of God when we do.

Galatians 5:19-21 ESV  Now the works of the flesh are evident: sexual immorality, impurity, sensuality, idolatry, sorcery, enmity, strife, jealousy, fits of anger, rivalries, dissensions, divisions, envy, drunkenness, orgies, and things like these. I warn you, as I warned you before, that those who do such things will not inherit the kingdom of God.

Ephesians 4:30-32 ESV  And do not grieve the Holy Spirit of God, by whom you were sealed for the day of redemption. Let all bitterness and wrath and anger and clamor and slander be put away from you, along with all malice. Be kind to one another, tenderhearted, forgiving one another, as God in Christ forgave you.

The good news is that the Holy Spirit is more than willing to personally show us how we ought to think and feel about things. The mind that is governed by the Holy Spirit will experience God’s renewal and a “new self” – as well as emotions such as love, joy, and peace in any circumstance.

Romans 8:6-8 NIV  The mind governed by the flesh is death, but the mind governed by the Spirit is life and peace. The mind governed by the flesh is hostile to God; it does not submit to God’s law, nor can it do so. Those who are in the realm of the flesh cannot please God.

Galatians 5:22-23 ESV  But the fruit of the Spirit is love, joy, peace, patience, kindness, goodness, faithfulness, gentleness, self-control; against such things there is no law.

But first, we need to set aside our own human understanding and entrust our emotions to His leadership – both on a conscious as well as a subconscious level.

Proverbs 3:5-6 ESV  Trust in the Lord with all your heart, and do not lean on your own understanding. In all your ways acknowledge him, and he will make straight your paths.

Understanding our subconscious (emotional) minds

Our brains comprise both a conscious and a subconscious mind.

Simply put, the conscious part of our minds is the one that we are fully aware of and which we use to process, compare, and analyse information from our environment. The subconscious part is the one that we are not fully aware of, which influences all our actions and feelings. It is said to account for 90% of our decisions.

The subconscious mind is the powerhouse behind our thoughts, feelings, perceptions, and beliefs. It is the source of all our emotions, such as fear, disgust, anger, and sadness. It never sleeps and can process 11 million pieces of information per second, compared to 40 pieces per second in our conscious minds, according to the article, Your Brain Sees Even When You Don’t.

The subconscious part of our brains, however, does not analyse or judge what we are exposed to. It simply records and stores whatever it senses as data, without a conscious filter for truth or falsehood, good or bad. The more we are exposed to something, the higher in priority it becomes. The subconscious mind learns by repetition, not by logic. Over time, we form many deeply imprinted subconscious impressions that form the foundations for our beliefs and values.

We absorb much more “subconscious data” than we realise. Our brains have the potential to store between 100 terabytes and even possibly 2.5 petabytes of data, according to a range of neuroscience estimates. That is a massive amount of “subconscious data”.

When we choose to follow Jesus, it is not only our conscious minds that we need to renew. We also need to renew our subconscious minds, since that is what ultimately drives our behaviour. This is by large, what the Bible refers to as the “flesh” or the “old self” that makes us inclined to sin over and over again on auto-play. In order to be freed, we need to “crucify” all our ungodly subconscious patterns and “bring them to nothing”.

Romans 12:2 ESV  Do not be conformed to this world, but be transformed by the renewal of your mind, that by testing you may discern what is the will of God, what is good and acceptable and perfect. 

Romans 6:6 ESV  We know that our old self was crucified with him in order that the body of sin might be brought to nothing, so that we would no longer be enslaved to sin.

Most of our adult subconscious data can be readily retrieved and submitted to God.

The challenge is that the subconscious data from our childhoods is usually hidden from our conscious awareness as a result of how our brains have developed. It is also part of our flesh that causes most followers of Christ to stumble.

Our subconscious data from our first eight years of unfiltered emotions

Our ability to consciously assess and analyse everything we see, hear, and feel only began about the age of eight, as our critical, logical minds began to develop. Before that, our subconscious minds were in charge.

This means that during the first eight to ten years of our lives, we would have witnessed many social cues and felt many emotions that we had no real cognitive ability to interpret or understand. They were simply taken as fact. Perceptions and feelings were taken as reality. Childlike ideas, self-beliefs, values, inner vows, and fears took root.

As people created in God’s image, children need more than just physical food and shelter. Our souls needed to be fed and nurtured emotionally too. Children need to be regularly given physical affection, told that they are loved, and tenderly nurtured and disciplined by strong, sensitive, and secure parent figures. Unfortunately, this never happens perfectly. It is virtually impossible.

As young children, we may not have had the cognitive ability to express our emotional needs but we would have instinctively felt when something was amiss. One might describe this as a “thirst” in our souls that will eventually manifest later as inbred feelings of anxiety, restlessness, grief, emptiness, or even anger. We can remain emotionally “thirsty” all our lives – until we invite the Holy Spirit to come heal us and deliver us from our inbred anxieties.

John 7:37-39 ESV  On the last day of the feast, the great day, Jesus stood up and cried out, “If anyone thirsts, let him come to me and drink. Whoever believes in me, as the Scripture has said, ‘Out of his heart will flow rivers of living water.’” Now this he said about the Spirit, whom those who believed in him were to receive, for as yet the Spirit had not been given, because Jesus was not yet glorified.

Child anxiety occurs on different levels. At one end of the spectrum is outright abuse where children are violated physically, sexually, mentally, and emotionally. On the other end is parental ignorance or neglect, where a child is starved of the necessary parental affection and emotional security, whether intentionally or not.

The subconscious memory of such painful childhood experiences can stay with us for life. No matter how much we may prosper later in life, we don’t feel entirely satisfied. Our spirits can still feel heavy, unfulfilled, or crushed but we won’t be able to really explain why.

Proverbs 15:13 ESV  A glad heart makes a cheerful face, but by sorrow of heart the spirit is crushed.

Addressing our subconscious emotions from childhood

Our childhood memories will invariably comprise a substantial portion of our subconscious minds.

While we can choose not to consciously think about them today, our subconscious minds will never forget our experiences. Databanks of subconscious negative emotions that are linked to our childhood memories, such as fear, shame, resentment, bitterness, and hatred for instance, will hinder us from loving God and others fully.

The apostle Paul talks about how to love others and flourish in our spiritual gifts in 1 Corinthians 12 and 13. In these chapters, he also talks about how we need to “put away our childish ways”. We only continue to speak, think, and reason “as a child” because our emotional maturity has been stunted by unhealthy patterns produced in childhood. We find ourselves instinctively resisting God like disobedient sons and daughters.

1 Corinthians 13:11-12 NLT  When I was a child, I spoke and thought and reasoned as a child. But when I grew up, I put away childish things. Now we see things imperfectly, like puzzling reflections in a mirror, but then we will see everything with perfect clarity. All that I know now is partial and incomplete, but then I will know everything completely, just as God now knows me completely.

To put our childish ways away for good, we need to confess our pains and the ways that we too had sinned against our own family members as a result. There will be some childhood experiences that we can talk about as if they just happened yesterday and others that will be shielded from our conscious memory. The latter is often a result of a few things.

As children, we may have:

• Hardened our hearts through emotional suppression, unforgiveness, bitterness, or hatred. We label the adults who hurt us as “bad” and continue to hate them. | Proverbs 28:14 ESV  Blessed is the one who fears the LORD always, but whoever hardens his heart will fall into calamity.
• Numbed our feelings as a means to ignore the pain in our hearts. We mask our pain, put on a smile, and pretend that “everything is okay”. | Proverbs 28:13-14 ESV  Whoever conceals his transgressions will not prosper, but he who confesses and forsakes them will obtain mercy.
• Chosen to sleep things over in our attempt to bury and forget our pain. We dull our senses and go through life “semi-conscious”. | Ephesians 5:11,13-15 ESV  Take no part in the unfruitful works of darkness, but instead expose them. But when anything is exposed by the light, it becomes visible, for anything that becomes visible is light. Therefore it says, “Awake, O sleeper, and arise from the dead, and Christ will shine on you.”  Look carefully then how you walk, not as unwise but as wise,
• Grown up in families that worship false gods. As a result, Satan “blinds our mind” and blocks our childhood memories. | 2 Corinthians 4:4 ESV  In their case the god of this world has blinded the minds of the unbelievers, to keep them from seeing the light of the gospel of the glory of Christ, who is the image of God.

Whatever the case may be, we can rejoice that the Holy Spirit will guide us on the path of recovery and healing when we ask Him to.

The Holy Spirit as Counsellor and Healer for subconscious childhood emotions

Trained biblical counselors can help us identify some of these “childish ways” after a number of sessions, but only the One who created us can give us new life. God has been with us all our lives and knows us completely – and He is full of compassion towards us.

Psalm 100:3-5 ESV  Know that the Lord, he is God! It is he who made us, and we are his; we are his people, and the sheep of his pasture. Enter his gates with thanksgiving, and his courts with praise! Give thanks to him; bless his name! For the Lord is good; his steadfast love endures forever, and his faithfulness to all generations.

Job 31:4 ESV  Does not he see my ways and number all my steps?

Praise God that the Holy Spirit will help us retrieve and remember long-forgotten childhood memories from our subconscious minds when we cry out to Him for His help and healing. When this happens, we will instinctively recognise the unhealed emotional wounds from childhood as they come back up to the surface again. 

John 14:26 ESV  But the Helper, the Holy Spirit, whom the Father will send in my name, he will teach you all things and bring to your remembrance all that I have said to you.

Psalm 107:19-20 ESV  Then they cried to the Lord in their trouble, and he delivered them from their distress. He sent out his word and healed them, and delivered them from their destruction.

This can be an uncomfortable aspect of having our subconscious minds renewed, as we confess our childhood disappointments – but it is a crucial component of growing in spiritual maturity.

God will shine His Light straight into the broken areas of our hearts from long ago and heal us, as long as we are willing to humble ourselves before Him. We do this through prayer and fasting, and being still before God. As He brings back our memories, it is our responsibility to confess the negative emotional imprints from childhood that continue to steer our adult hearts and repent of the ways we responded sinfully as children. This is where the Holy Spirit will bring us new life in our deepest subconscious psyche. This is also when greater spiritual freedom can begin.

Titus 3:3-5 NLT  Once we, too, were foolish and disobedient. We were misled and became slaves to many lusts and pleasures. Our lives were full of evil and envy, and we hated each other. But—  When God our Savior revealed his kindness and love, he saved us, not because of the righteous things we had done, but because of his mercy. He washed away our sins, giving us a new birth and new life through the Holy Spirit.

For some real-life examples of how followers of Jesus Christ have received greater freedom and peace as they sought God, please refer to the following testimonies:
Jesus shows lawyer true rest.
Jesus reveals legal advisor’s hidden self-rejection.
Jesus replenishes and heals architect.

Testimony: Turning from relating to God with the conscious mind to the subconscious (heart)

“Ever since my growing up years, I have had a subconscious drive that I needed to be obedient, good, smart, respectful to elders, and be as good as “most people of my age”. That constant chase to be better was draining and endless.

Even after I became a Christian, I held on to those expectations as to what I needed to do in order to be on top of my Christian “responsibilities”.

During inner healing and deliverance prayer, I was reminded that the things I was taught to be right as a kid were not necessarily what God sees as right. The world teaches us to be smarter in academics and career, yet the Bible says “The fear of the Lord is the beginning of knowledge” (Proverbs 1:7). The world teaches us to be “a good girl,” but Jesus said “Why do you call me good? No one is good except God alone.” (Mark 10:18).

God’s words released me from standards that were not from Him, and reminded me to always go back to God for the truth.

As we were praying based on God’s truth, a prayer counsellor asked if I was praying to God from the heart, or whether I was trying to say the right things that I believed God would like to hear. I paused, surprised that it’s hard to tell, because I was so used to acting in the right way or giving the model answers.

I tried to pray again, willing myself to sound more sincere and emotion-driven, but when the words came out, we sensed that it was still from my head, thinking what a genuine prayer should sound like.

I realised that I was still trying to use my limited knowledge to do better, so I went before God and asked the Holy Spirit to teach me how to pray.

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. (Romans 8:26)

It took a while as I called to God and asked Him to soften and open my heart, to remove all the rules and expectations that were blocking me from Him. When I finally admitted to God that I couldn’t do it, and could only rely on Him, the tears came and I felt a relief in my heart, as if I was letting go of a burden that I wasn’t meant to carry.

It was quite eye-opening to recognise that often, I had prayed to God from my head rather than my heart.

Now in my daily prayers, I find the Holy Spirit prompting me from time to time, continuing to guide me how to connect to God with all my heart.”

May this sharing be a blessing to you as you seek to love God with all your heart and follow the Holy Spirit in the ways He directs your mind.

Also, see
Renewing the spirit of our minds.
The importance of emotional healing.
Parent wounds need to be healed.
Vocabulary to unplug buried emotions and receive God’s healing.