Getting Below The Waterline The Role of Inner-Healing Prayer in Spiritual Transformation

In the days following my husband’s death, I desperately sought God’s comfort in the Scriptures. After an eleven-year battle with Multiple Sclerosis and all the humiliation, fear, hardship, and losses that go with it, my faith was on the fragile side. I needed solace, the kind only God could give.  So I went to the Psalms. Isn’t that where God’s children always find consolation?

But I found no consolation there. On the contrary, in fact. One day I was reading Psalm 91, the psalm just about every Christian turns to in times of fear or discouragement:

Surely he will save you
from the fowler’s snare
and from the deadly pestilence.
He will cover you with his feathers,
and under his wings you will find refuge;
his faithfulness will be your shield and rampart.
You will not fear the terror of night,
nor the arrow that flies by day,

nor the pestilence that stalks in the darkness,
nor the plague that destroys at midday.
A thousand may fall at your side,
ten thousand at your right hand,
but it will not come near you.
You will only observe with your eyes
and see the punishment of the wicked.

If you say, “The Lord is my refuge,”
and you make the Most High your dwelling,
no harm will overtake you,
no disaster will come near your tent.[1]

I didn’t want to admit it, but the psalm made me feel angry. My husband had not been saved from the deadly pestilence or the destroying plague. My whole family had experienced plenty of terrors by night, and plenty of arrows by day. Disaster had come near our tent. More than just near, it had invaded our tent, taken my husband’s life, and left my son and me wounded and bereft. God did not feel like a refuge. Actually, reading the psalm made me feel as if God were mocking me.

Hadn’t I loved God enough to deserve His protection? I wondered. Had I failed Him and in the process, nullified His promises? If God had allowed so much pain and suffering to happen to my family and me already, how did I know there wasn’t more or even worse to come? I felt as if I were just waiting for the other shoe to drop.

Mind you, I admitted these thoughts to no one, hardly even to myself. I was a leader in full-time ministry, after all. I’d been serious about my walk with God for decades. I invested myself in helping others to grow spiritually. How could I possibly admit such thoughts and feelings? They seemed almost blasphemous to me. I didn’t want to jeopardize the faith of others.

About that time, a man in my church whom I’d only met on a couple of occasions mentioned a healing prayer ministry he was part of. With no knowledge of my spiritual crisis, he offered, “If you ever want to have somebody pray with you and help you listen to God, we have people who do that. Just let me know.”

At that point in my spiritual journey, listening to God was something that was still relatively new to me. For much of my Christian life, I didn’t know how to hear God speak to me personally. Although I had puzzled over Scriptures like John 10 that assured me that Jesus’ sheep hear His voice,[2] my prayers had been mostly one-way monologues. And the impersonality of that seemingly one-way relationship left me feeling lonely and detached from God. But during the hardest years of my husband’s illness, God had mercifully taught me how to listen to His voice. Through experience, He proved to me that I could call to Him and He would answer me,[3] and that I could come to Him with my ears wide open and in listening, I would find life.[4] He helped me to understand that He really does call me friend,[5] and that He enjoys it when I invite Him to have conversation with me, Friend to friend.[6]

I don’t think I would have survived the years of illness, loss, and relentless caregiving if I hadn’t learned to hear my Father’s tender voice. Time and time again I was amazed by His almost unnervingly personal care for me as He patiently responded to my anger and fear, and gently comforted me and fathered me. As my ability to discern His voice grew, so did my relationship with Him. God became more personal and intimate—and thus more indispensable to me—than He had ever been before.

But in spite of having heard God and even dialogued with Him in deeply personal, relational ways, He seemed pretty silent in those dark days after my husband’s death. The warm conversations we’d had previously seemed like ancient history. So when Jack asked me if I would like somebody to listen to God with me, I was open. I wasn’t hearing much from God on my own, but maybe listening with others could help me to re-connect. I had no idea what to expect, but I set up a time to pray with him and a woman from the church’s healing prayer team.

Healing prayer, it turned out, was different from any other kind of prayer I’d ever been involved with. But even though it was a stretch for me, it made complete sense. Using listening prayer as a foundation, it is a way of asking Jesus to do for people now, in our generation, the kind of ministry that Isaiah 61 (and Luke 4) describe Him as doing—binding up broken hearts, freeing captives, releasing prisoners, comforting all who mourn, exchanging despair for praise.

My prayer partners explained that they had no agenda except to ask Jesus to do His healing work. They said they would focus our prayer time on asking God what I needed and how He wanted to meet me. They asked me a few questions, equivalent to a medical doctor asking, “Where does it hurt?” Then they explained to me that they would ask God a question and invite Him to respond to me. He might bring up a memory or impression, perhaps He would stir up a painful emotion. He might bring to mind words that had been spoken to me, or maybe a verse of Scripture. Maybe He would give me a picture. Whatever came to mind I was to report. If we weren’t sure if it was from God or not, or if we didn’t know what it meant, we would simply ask Him to confirm or clarify.

In the process of listening to God in that manner, He did speak. He revealed early memories—long before the ordeal with my husband—of times when I had felt unprotected and vulnerable. He helped me to see that long before adulthood I had come to believe that those who are supposed to protect me, won’t. That if I don’t look out for myself, no one else will. He helped me to see how, subconsciously, I’d transferred these beliefs to Him, too. Without even knowing it, I’d come to believe that God would not protect or help me, that I had to take care of myself. Was it any wonder that when I needed God the most, I couldn’t find Him? I’d built my life around those devastating, isolating lies, so that I had no real expectation that He would rescue me. Sure, I “believed” Psalm 91 intellectually, but in my deepest heart, I doubted.

When those lies were exposed, I was able to confess them and ask God’s forgiveness for doubting His love and care. I was able to see and declare the truth that God is for me and He helps those who call to Him in faith. Over time, I was able to forgive the ones who had failed to keep me safe and had set me up to believe awful lies about God and life.

Healing for me wasn’t one quick prayer session. It involved a series of times similar to what I just described in which God revealed to me the obstacles that were standing in the way of my trusting Him. Over a period of months, as one by one I dealt with them, my confidence in God’s loving care grew so that now I can read Psalm 91 with peace and hope.

Inner-Healing Prayer’s Part in Spiritual Formation

My personal experience with inner-healing prayer, both offering it to others and receiving it, has prompted me to believe that it plays a helpful, if not critical, role in spiritual formation. In my case, I desperately wanted to trust God. I was miserable when I dreaded the future because I couldn’t bring myself to trust in His care for me. My struggle filled me with guilt and shame. I hated feeling suspicious of God while all the while professing my faith in His goodness. So I read books on faith. I memorized Scriptures about His goodness. I confessed (over and over and over) my fear. I gritted my teeth and tried to “just do it.” I learned so much about what it meant to trust God that I suspect I probably could have given a convincing inspirational talk or written a powerful devotional about the faithfulness of God. But no matter how firmly my head was convinced, my heart still struggled.

As others have invited me to pray with them for inner healing, I’ve discovered that I was by no means alone in my spiritual frustration. Many of us have deep-rooted wounds that get in the way of our spiritual transformation. My issues of doubting and distrusting God are far more common than I realized. But there are many others: inferiority, shame, perfectionism, addictions, obsessive and compulsive behavior, anxiety, gender confusion, people-pleasing, body image issues, and more. All of these are serious barriers to our ability to experience God and grow in Jesus’ likeness. And all of them are nearly impossible to address by conventional means of discipleship such as Bible study, Scripture memorization, or petition-based prayer.

Rusty Rustenbach, director of pastoral care and counseling for The Navigators and author of A Guide to Inner-Healing Prayer: Meeting God in the Broken Places, describes how, as a seasoned counselor, missionary, and disciple-maker, not only was he unable to help the people he ministered to get past these obstacles—he could not get past them himself. As a boy, he had not received from authority figures the affirmation he needed—which led to insecurity, people-pleasing, and periodic overreactions to triggering events that continued into adulthood. He wanted to be free from those inner attitudes and weights —but the spiritual disciplines he tried weren’t setting him free. Then one day he read Psalm 18:9: “He brought me forth also into a broad place; He rescued me because He delighted in me.”[7] Yeah, I’ll bet God delights in me, Rustenbach mused, cynically. No, He puts up with me because He’s stuck with me.”[8]

A friend talked to Rustenbach about listening prayer (in 1997, before much had been taught or written about the inner-healing aspect of listening prayer) and Rustenbach reluctantly agreed to try it. He really didn’t expect anything to happen, but God surprised him. “Rusty, I am for you… for you and not against you. You belong to me I chose you to belong to Me because I love you with an everlasting love. You are Mine!”[9] That intimate encounter with God was deeply healing to Rustenbach; as he relates the story today, fifteen years later, his eyes still fill with tears. And now, listening and inner-healing prayer has become the foundation of his fruitful ministry with The Navigators.

“As our global society increases in complexity, size, and brokenness, growing numbers of people struggle with issues that seem impervious to traditional ministry methods.”[10] Rustenbach says. Spiritual disciplines are useful and necessary, but inadequate to deal with issues that are hidden “below the water line.”[11]

Often a person is not even aware of these below-the-surface wounds. Nevertheless, he or she may feel trapped by unwanted but automatic reactions, unhealthy habits, and negative thought patterns. In persons who have walked with the Lord for a long time these are especially troubling. After all, intellectually, they believe the right things. They have good theology. But there is a head-heart schism. What they believe in their heads does not work itself out in their lives, in spite of counseling , effort, or traditional forms of prayer. These kinds of wounds require a touch from Jesus, a manifestation of God’s grace. We need God to show us where the problem is rooted—and we need Him to bring the healing.

This process does not require a person to probe deeply into his or her past. Such introspection, as many of us have learned the hard way, often isn’t helpful, and can even be harmful. Through difficult experience we understand that “the heart is hopelessly dark and deceitful, a puzzle that no one can figure out.”[12] But God is able to lovingly, gently, objectively sort out what we cannot. “I, God, search the heart and examine the mind. I get to the heart of the human. I get to the root of things. I treat them as they really are, not as they pretend to be.”[13]

Assumptions and Principles of Inner-Healing Prayer

There are different models of inner-healing prayer, most of which rely on some variation of these assumptions and principles:

  • A person experienced an emotional wounding, often in childhood (e.g. abandonment by a parent, real or perceived rejection by significant people, sexual, verbal, or physical abuse, loss, deprivation, etc.).
  • Lies about God, self, or the way the world works were believed as a result of that traumatic, painful or disappointing experience (e.g. “If I let people know who I really am, they won’t like me”).
  • Vows may have been made in an attempt to protect the person from future hurt (e.g. “I’ll never trust a man again”).
  • Generational patterns may have been inherited (such as patterns of fear, a poverty mindset, and so on).
  • As we practice listening prayer, the Holy Spirit speaks in our minds or hearts, through pictures, the stirring of emotions, words, symbols, or other creative and very personal means.
  • Usually God takes us back to memories from childhood where the wounding took place. He helps us to see what happened to our souls at that time, exposing lies we came to believe, unbiblical vows we made, faulty strategies for living that we adopted, and perhaps the pronouncements others made over us.
  • We confess these lies, vows, and so on, to Him and ask Him to reveal truth. As we embrace the truth He reveals, our minds are renewed and we are freed from the emotional bondage that hindered our spiritual growth and freedom. We stand with Jesus, Way, Truth, and Life, and declare our independence from the father of lies.
  • Sometimes we see Jesus with us in the memory of the painful event.  He may speak words of truth or offer comfort that usually is deeply moving and penetrating.
  • With His help, (sometimes over time rather than immediately) we forgive the ones who wounded us, both for the actual offense, as well as for the consequences we have experienced as a result of that offense.
  • By replacing lies with truth and forgiving those who hurt us, we close off areas of access to the enemy. He can no longer energize those places for us.
  • We adopt our true identity in Christ rather than the false identities we assumed because of the lies we believed and the wounds we were compensating for.
  • We expect that the Wonderful Counselor actually will meet us and touch us when we invite Him into our wounded places. When we invite Him, He will come, and He will heal.

Recently I had a conversation with a young Christian medical student who is seeking to understand God’s role in healing. He cited research that supports the efficacy of prayer for soul healing. That wasn’t surprising, he told me, since prayer is a form of catharsis, allowing for the release of painful emotions so that healing can occur. I agreed with him that pouring out our hearts to God is indeed cathartic. What kinder, wiser Listener could we ever have than our Abba, Father, who made us and redeemed us and constantly watches over us in love? But there’s more, I told him. Inner-healing prayer is supernatural. God actually does something when we invite Him to heal our hurting hearts. Somehow, He enters into our pain with us and releases us from it with no less power than when He healed 2,000 years ago.

As Richard Foster so aptly puts it, “Don’t you know that Jesus Christ, the Son of God, who lives in the eternal now, can enter that old painful memory and heal it so that it will no longer control you?”[14]

Healing Prayer Resources

Inner-healing prayer can be a helpful adjunct to spiritual direction, counseling, discipling, and pastoral care, although depending on where you live, it may be difficult to find a good practitioner. This form of soul-care, as in any other, should be left only to those who are reliably trained, spiritually and emotionally mature and healthy themselves, biblically sound, in accountability relationships with other Christians, and with a proven record of helping others find healing and freedom. If you cannot find someone like that in your community, you may want to consider receiving training yourself. There are several options:

The Pastoral Care Team of The Navigators (Rustenbach’s organization) offers listening and healing prayer seminars several times a year in Colorado Springs, Colorado, and elsewhere, by invitation.

Ministries of Pastoral Care (founded by Leanne Payne, who has since retired) offers training each summer at Wheaton College, in Illinois.

The International Association for Theophostic Ministry (founded by Ed Smith) offers comprehensive training resources for individuals or groups (such as a church prayer team).

Christian Healing Ministries (founded by Francis MacNutt) offers conferences, seminars, a healing prayer school, and internships, along with printed and video resources for basic or in-depth training in healing prayer of all kinds.


[1] Psalm 91:3-10, NIV

[2] John 10:3-4, 8, 16, 27

[3] Jer. 33:3

[4] Is. 55:3

[5] Jn. 15:15

[6] Rev. 3:20, NLT

[7] NASB

[8] Rusty Rustenbach, teaching at the Listening and Healing Prayer Seminar, The Navigators, Colorado Springs, May 18-19, 2009

[9] Rusty Rustenbach, A Guide for Listening & Inner-Healing Prayer, Colorado Springs, CO: NavPress, 2011, p. 22.

[10] Ibed, p. 165

[11] Ibed, p. 103

[12] Jer. 17:9, MSG

[13] Jer. 17:10, MSG

[14] Richard J. Foster, Prayer: Finding the Heart’s True Home. New York: HarperCollins, 1992, p. 205.

Cynthia Hyle Bezek:
        Cynthia Hyle Bezek facilitates inner-healing prayer through her local church’s prayer ministry. She is author of Prayer Begins with Relationship, former editor of Pray! magazine, and blogs about prayer at cynthiaprayblog.wordpress.com. She currently serves as editorial director for Community Bible Study.

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  • Maggie Carnes

    This is an excellent article on inner healing prayer. Thank you for sharing your healing and offering resources. You might also want to view the website of an international organization that I belong to, OSL: The Order of St Luke. http://www.orderofstluke.org

  • http://pnpontheroad.blogspot.com Patrick Watters

    So much brokenness, so few “healers”
    Lord increase workers for your harvest
    Empower Your priesthood of all believers
    Send us out, Your wounded healers.

    PnP On The Road

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    Thanks EMILIANO BABARAH_USA