Spiritual Roots Beneath: Trusting God With What’s Hidden

Spiritual Roots Beneath: Trusting God With What’s Hidden

By Sherita Jones | The Anointing Grace

It’s strange how something as ordinary as a plant’s root system could unravel such a deep, personal, spiritual truth in me. But this is how God speaks through the simple to reveal the profound.


I wasn’t looking for a sermon when I started researching root systems. I was simply journaling my prayer, weeping before God, desperate for answers about why healing feels so slow, why my heart feels so heavy, why breaking free feels more like suffocating than deliverance.


God led me straight to rootsTaproot and Fibrous root systems and suddenly, it was as if He laid out the blueprint of my entire life beneath the soil of my soul.


What’s Beneath the Surface Affects Everything Above It


Taproot systems reach deep into hidden places. They anchor plants, draw water from depths unseen, and store nutrients for survival.


Fibrous root systems spread wide, creating dense networks near the surface, intertwining with anything nearby, absorbing whatever’s available, competing for space, nutrients, and water.


And isn’t that exactly how trauma, pain, neglect, rejection, and abuse behave beneath the surface of our lives?


These aren’t just “things we’ve been through. They become roots. They anchor in our hearts. They spread into our thoughts, our choices, our relationships, even our health.


These bad roots don’t just stop at the heart or the mind, they creep into the our body systems and our organs, weakening what God designed to function in harmony. 


The lungs, spiritually, represent the breath of life and the capacity to rest in God’s peace. Trauma roots itself here, manifesting as anxiety, panic, breathlessness, not just physically, but spiritually robbing us of the ability to breathe deeply in trust. 


The liver, in biblical symbolism, often connects to cleansing and bitterness. When roots of rejection, abandonment, or unforgiveness are buried deep, they congest the liver’s function spiritually, making it hard to filter what’s clean from what’s toxic in our thoughts, emotions, and decisions. 


The kidneys, tied to the processing and releasing of waste, represent discernment and wisdom in Scripture. When pain pollutes these areas, we spiritually struggle to discern rightly, to release offense, to let go of what no longer serves us. 


The enemy’s roots tangle through these organs beneath the surface unseen but deeply affecting how we live, how we move, how we hope. Yet God, in His mercy, gently untangles these roots, not only freeing our hearts but restoring our breath, our discernment, and our ability to process life through His Spirit.


The Problem with Entangled Roots


In nature, roots that grow too close invade each other’s space. They compete for resources. They choke out life. The stronger root dominates. The weaker root starves. Invasive roots like bamboo or willow trees spread far beyond their borders, creeping into places they were never meant to reach, foundations, pipes, neighboring plants.


Spiritually, I’ve lived this. The root of rejection snaking into my relationships. The root of abandonment creeping into my ability to trust. The root of neglect strangling my self worth. The root of fear infiltrating my faith.


What started beneath the surface became a system of emotional and spiritual erosion. Like plants fighting underground for water, my past and my future have been at war for my nourishment, for my survival.


The Garden of My Heart: God Begins to Uproot


Acknowledgement is the first painful cut of the Gardener’s tool. God had to show me, these roots are deeper than I thought. They’ve spread wider than I realized. They’ve become tangled with parts of my life I never expected.


Healing doesn’t start by pretending the roots aren’t there. It starts by letting God reveal them. There’s stuff buried deep even I can’t see. Only God can dig there.


“The heart is deceitful above all things, and desperately wicked: who can know it?”

‭‭Jeremiah‬ ‭17‬:‭9‬ ‭KJV‬‬


Uprooting Hurts Because Roots Don’t Let Go Easily


The process feels violent at times. Memories resurface. Old wounds reopen. Emotions I thought were dead scream to be heard.


God uproots through surrender. Through repentance. Through forgiveness. Through releasing what’s killing me softly: bitterness, shame, unforgiveness.


Hebrews 12:15 warns us: “looking diligently lest any man fail of the grace of God; lest any root of bitterness springing up trouble you, and thereby many be defiled;”


But tearing out roots leaves voids. Spaces. Wounds. That’s when the enemy whispers “You’re going backward.” “You’re breaking down, not breaking free.”


No, beloved. This is necessary. This is surgical. This is sacred.


When God Plants New Roots in Broken Soil


Uprooting is only half the work. Replanting is where healing breathes again.


Ephesians 3:17-19 says:

“that Christ may dwell in your hearts by faith; that ye, being rooted and grounded in love, may be able to comprehend with all saints what is the breadth, and length, and depth, and height; and to know the love of Christ, which passeth knowledge, that ye might be filled with all the fulness of God.”

God doesn’t just leave holes where pain used to live. He fills them with truth: You are chosen. You are loved. You are worthy. You are whole. You are mine.


Like Psalm 1:3“And he shall be like a tree planted by the rivers of water, That bringeth forth his fruit in his season; His leaf also shall not wither; And whatsoever he doeth shall prosper.”

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These aren’t shallow roots anymore. They’re deliberate. Deep. Anchored in truth, not trauma.


Why Healing Feels Like a Back and Forth Battle


Roots don’t release easily. Neither does pain. Some days feel like progress. Others feel like relapse. But healing isn’t linear, it’s layered. Some roots break with tears. Others with prayer. Some with fasting. Some only with time.


John 15:1-2 teaches: The Father prunes what doesn’t bear fruit, so we may produce more.


“I am the true vine, and my Father is the husbandman. Every branch in me that beareth not fruit he taketh away: and every branch that beareth fruit, he purgeth it, that it may bring forth more fruit.” John‬ ‭15‬:‭1‬-‭2‬ ‭KJV‬‬


And pruning hurts.

It exposes.

It looks barren before it looks beautiful.


The Tenderness of God’s Hands in My Healing


Separating tangled roots in nature requires patience. Precision. Time. It risks shock to the plant. It demands aftercare. Water. Nourishment. Shelter.


God is no less gentle with me. After every painful separation, He waters me with His Word. He nourishes me with His presence. He shelters me in His arms.


This process doesn’t just heal the surface, it heals the organs beneath. The lungs from anxiety. The heart from heaviness. The mind from fear. The spirit from unrest. Every system impacted by roots is being rewired, restored.


Protecting the New Roots


Like barriers in gardens protect from invasive species, I must protect this healing: Guard my prayer life.Stay rooted in the Word. Surround myself with those who speak life, not death. Refuse toxic soil. Refuse old patterns.


Encouragement for Those Like Me, Still in Process


I share this not because I’ve arrived, but because I see God’s hand even in the dirt. He’s not punishing me. He’s preparing me. He’s not angry. He’s attentive. He’s not distant. He’s digging close.


Isaiah 61:3 whispers:

“to appoint unto them that mourn in Zion, to give unto them beauty for ashes, the oil of joy for mourning, the garment of praise for the spirit of heaviness; that they might be called trees of righteousness, the planting of the LORD, that he might be glorified.”

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Final Thoughts: Healing Takes Time, But Roots Are Eternal


I didn’t fully understand this process, but now I understand: roots determine everything. Where I’m planted, what I absorb, how I grow, whether I flourish. God’s after the roots because He’s after the fruit. Not temporary. Not seasonal. Eternal. Unshakable. Holy.


I am becoming, and I’m rooted in His love. Planted in His truth. Nourished by His Word.

And nothing planted by the Lord shall wither.


This is my story beneath the soil.

This is The Anointing Grace.

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