Quiet Time When You Doubt God’s Existence

Posted by Naomi Vacaro on

Doubting Doubt
Emily Miller

I’ve been a follower of Jesus since I was seven. I grew up surrounded by Christians and was well-saturated in the Gospel. My dad frequently challenged me with hard questions, wanting me to know why I believe what I believe. He wanted my faith to be built on Jesus and not on the faith of my family.

This was helpful to me when I moved to the Pacific Northwest and faced an onslaught against anything remotely Judeo-Christian. At my job, I talked about faith and evolution with my customers and argued the reliability and relevancy of scripture with my co-workers. I urged friends to read the Bible for themselves and not depend on their pastor or parents for their faith.

Then I had a few experiences with death and suffering and several years of depression. Doubt roared in and battered me with wave after wave of fear and questions. For four years I would read the Bible for an hour each morning while God felt like a fairy tale and I felt like a fraud.

I’m likely not the only one with seasons or recurring bouts with doubt. Doubt is painful, disorienting, and even panic-inducing. When we wonder if God is even real, reading the Bible can be incredibly discouraging. Yet, spending time with Jesus as we wrestle through doubt is more important than ever!

Doubt leaves us with three options:
First, we can hide from our doubts, pretend they aren’t there, and shove the nagging thoughts aside. Yet in this approach, reading the Bible might cause uncomfortable questions to flare up, so we’ll likely start avoiding quiet time.
Second, we can surrender to our doubts, deconstruct our faith, become atheists or agnostics, or run to another religion. In this case, to continue reading the Bible is meaningless.

Third, we can decide to doubt our doubts, ask the questions we know we need to be answered and keep asking God to help us as we keep reading the Bible day after day. I went with the third way and it was a long, painful, tiring, and not at all comforting, process. But in the end, doubt was replaced with a growing assurance in the God-Man, Jesus Christ.

Now when doubt flares up, I ask two questions:

Why am I Doubting?

Doubt often seems like truth itself coming to shatter our former beliefs. But, our doubts are rarely based on objective truth and we are often completely oblivious to our heart’s motivations. This is why it is important to assess where our doubt might be coming from.

Sometimes doubt (and even our faith!) is rooted in our emotions. We believe when God feels real to us. When suffering shakes us, doctrines like hell and sin disturb us, and God feels distant; we doubt.

Doubt can be rooted in fear. Instead of an emotional response to a specific issue, these doubts come in the form of endless and unsolvable “what ifs”. We have a general sense that we’re likely wrong without any specific reasons or evidence. Since we could be wrong, we must be wrong. (Which is as silly as saying: “Since I could be right, I must be right”!)

Sometimes our doubt is rooted in desire. When we want (or even begin to do) what God forbids, His non-existence becomes all too convenient.

Sometimes our doubt truly is based in reason. How can what I believe be true when most people believe differently? Is the Bible accurate and true? Are science and the Bible incompatible? We doubt because we need to think more deeply about important questions and understand the reasons why we believe what we believe.
At all times we are also contending with a flesh that resists the truth, a world system that opposes Christ, and demonic spirits that seek to steal away peace, kill faith, and destroy souls. Satan is skilled and active in using our emotions, fears, desires, and reasoning to implant and inflame doubt.

How Do I Deal with this Doubt?

Knowing where doubt is coming from is essential in knowing how to wisely handle it.

When emotion fuels doubt, it’s key to remember that emotions don’t affect truth. Fact is fact no matter how we feel. The fight then is to patiently guide, endure, and even ignore our emotions until they settle down and better align with truth.

When doubt is from sheer, unspecific fear it’s helpful to remember that this kind of doubt is irrational. It doesn’t use evidence and no amount of evidence is ever enough. God could speak to us directly and we’d reason it away as a psychological break. This doubt takes the fact that our knowledge is limited and uses that as proof that our deepest fears are likely true. Fear is blind, faith is not. Faith invites us to find good and sufficient reasons to trust Jesus. Trust is the antidote to fear and so trusting Jesus with our fears is the only way forward.

When doubt is rooted in sinful desire, we deal with it by recognizing and calling out our own motives. It helps to look honestly at the long-term results of following those desires and realize that we tend to see what we want to see and overlook what we’d like to ignore. Choose to accept difficult truths over preferences. Our choice is to accept truth and run to Jesus or reject truth and run after our desires. If we choose to run to Jesus, He’ll be faithful; the temptation will lose strength and doubt will fade.

When doubt is coming from reason then we investigate! Don’t just read the Bible, study it! Read books dealing with each troubling question. Research how different worldviews deal with suffering, sin, existence, and meaning. Listen to debates between Christian and non-Christian thinkers. Ask Christians uncomfortable questions. Grow in recognizing and refuting logical fallacies. Gather historical, textual, scientific, psychological, existential, and pragmatic reasons why Christians believe that God exists and that the God of the Bible is the one true God.

When doubts relentlessly pummel us in cycles of thoughts that lead nowhere, it’s wise to assume that it’s a spiritual attack. Pray, sing hymns, memorize scripture, and bring fellow Christians in on your soul’s battle.

Friend, some of us are very straightforward. We don’t need books and arguments for why a chair will support our weight. We simply sit in the chair and find that it does. Others of us are deeply skeptical. We need to question and reason things out. Like Thomas, we need to place our fingers in the nail holes before we see the risen Savior. This Savior is very patient with us. He welcomes both the skeptic and the little child to seek, find, and taste that He is good.

In the depths of my doubts, as I searched for answers in every religion and worldview, my soul cried out “To whom will I go? You alone have the words of eternal life!” (John 6:68)

As I trusted Jesus I found Him more and more true, not just in theory but from experience.

I studied the chair, sat in it, and found that it bears the weight of my soul.

Helpful Resources for Times of Doubt:

  • Citizens and Saints songs “Doubting Doubts”, “Faith” “Fear”, “Madness”… every song by them.
  • “The Case for Christ” and “The Case for Faith” by Lee Strobel
  • “Christianity and World Religions: An Introduction to the World’s Major Faiths.” by Derek Cooper
  • Alisa Childers Podcast


Emily began having daily quiet time at the age of 13. This habit has been one of the few constants in her life as she transitioned from being a missionary kid in Mongolia to a barista in Oregon to a stay-at-home mom of 5 in central Florida. The Word of God has anchored Emily to Jesus through depression, struggles with doubt, health issues, and her son and daughter's cystic fibrosis.

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  • Thanxs Emily I Just Goggle Why Do People Doubt God And I Saw Yur Article And Rite Now I Am Really Struggling With Doubting God It Waz Extremely Helpful And Encouraging 2 Me May God Bless u Emily ✌️

    Rell on
  • Thank you for sharing this. It is exactly what I am feeling in this season and this is exactly what I needed to read. Thank you for pointing people in the right direction.

    Christi on
  • Thank you, my doubts are overwhelming me. I pray God will help me trust him fully. 🙏🏾🙏🏾😭😭

    Seeking him on
  • Thank you, my doubts are overwhelming me. I pray God will help me trust him fully. 🙏🏾🙏🏾😭😭

    Seeking him on
  • Struggling with whether I am a hypocrite. Do I really believe?

    Dianne M Eastlack on
  • Thank you Emily! Thank you for pointing us in the right direction, not just quick answers. Thanks for pointing us to Jesus.

    Ian Barnes on
  • Thanks for your encouragement, Em and CB! Love you both. (:

    Emily Ruth Miller on
  • Em, I had no idea you had wrestled through this same battle. It has been an ongoing spiritual wrestling match for me the last couple of years (with intermittent stretches of fear and doubt in previous years & seasons), and I’ve settled on knowing God is real—He exists. I know that by Him all other things exist. I believe Jesus to be the Savior the world desperately desires and needs. But so many years of spiritual/intellectual invalidation, trauma & a childhood hallmarked by the message that who I am is a disappointing mistake has led to utter dismay and doubt that the God of the universe sees, knows, and seeks relationship with me. That my years of faithful study and service were valued by a God so big feels impossible—why would He notice? What is a Father if he isn’t despising or demeaning or belittling? What does the tenderness of a deity feel and sound and look like? When the men in leadership cannot answer my questions (developed over hundreds of hours of scriptural study) and have only pat answers and disgust to offer… I find myself shouting at the sky, “Show me who You are! Tell me who I am!” To hear that He designed me with intention and tenderness feels impossible & uncertain, like rotten floorboards.

    That’s a long-winded way to say, “thank you.” I appreciate your transparency and, like a man crawling on his belly through a vast desert, I’m frantically grasping at the hope you’ve offered that there is relief and hope on the other side of this wasteland of grueling doubt. You’ve shone a light of possibility into my deep dread, and I am so incredibly grateful.

    Emily Gemin on
  • Thank you, Emily, for this excellent article addressing doubt and the reasons it might arise in a believer’s life,
    and for presenting very clear helpful and practical ways to confront doubts when they arise.

    CB Sprenger on

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