Sept 30 | When Doubt Makes Your Faith Stronger: Learning to Question Well
The Hidden Gift of Honest Questions
What if everything you've been told about doubt is wrong?
For years, many Christians have been taught that questioning your faith is a sign of spiritual weakness. That good believers don't struggle with uncertainty. That if you're truly saved, you'll never wrestle with whether prayer really works, whether God is truly good, or whether this whole Christianity thing is actually true.
But here's what might surprise you: some of the most faithful people in the Bible were also the biggest doubters.
In this comprehensive guide, we're going to explore how honest doubt isn't just acceptable in the Christian faith—it can actually become the pathway to a deeper, more resilient relationship with God. We'll look at Biblical examples of doubt, understand the difference between healthy questioning and destructive cynicism, and discover practical ways to navigate seasons of uncertainty without losing your faith.
If you've ever felt guilty about your questions, this post is for you. If you've ever wondered if your doubts disqualify you from being a "real Christian," keep reading. Because you're about to discover that you're in much better company than you ever imagined.
The Story That Changes Everything: Meeting Doubting Thomas
Let's start with one of the most misunderstood stories in the entire New Testament: the account of Thomas and the resurrection.
You probably know this disciple by his infamous nickname: "Doubting Thomas." For centuries, Christians have used his name as a cautionary tale about the dangers of skepticism. But when you read John chapter 20 with fresh eyes, something remarkable emerges.
What Really Happened After the Resurrection
Jesus had appeared to His disciples after rising from the dead, but Thomas wasn't present for that initial appearance. When the other disciples told him, "We have seen the Lord!" Thomas responded with one of the most honest statements in Scripture:
"Unless I see in his hands the mark of the nails, and place my finger into the mark of the nails, and place my hand into his side, I will never believe." (John 20:25)
At first glance, this seems like stubborn unbelief. But consider the context: Thomas's friends were claiming that a man he watched die brutally on a Roman cross was now somehow alive again. This wasn't a small claim. This was world-altering, reality-bending news.
Would you immediately believe such a story without evidence? Or would you, like any rational person, need proof?
Jesus's Surprising Response to Doubt
Here's where the story gets beautiful. Eight days later, Jesus appears again—and this time Thomas is present. But Jesus doesn't shame him. He doesn't lecture him about having more faith. Instead, He does something that reveals the true heart of God toward honest doubters:
"Put your finger here, and see my hands; and put out your hand, and place it in my side. Do not disbelieve, but believe." (John 20:27)
Jesus meets Thomas exactly where he is. He offers evidence. He invites investigation. He honors the request for proof.
This is one of the most compassionate moments in all of Scripture. Jesus essentially says, "You need to see? Then see. You need to touch? Then touch." He doesn't demand blind faith—He offers reasonable assurance.
And Thomas's response? "My Lord and my God!" (John 20:28) His doubt, when met with evidence and patience, transformed into one of the most profound declarations of faith in the Bible.
Understanding the Two Types of Doubt
Not all doubt is created equal. There's a critical distinction we need to understand between honest doubt and cynical doubt, and knowing the difference can literally save your faith.
Honest Doubt: The Seeker's Question
Honest doubt says, "I want to believe, but I have real questions that need real answers." It's characterized by:
Genuine seeking: You're actively looking for truth, not just trying to justify unbelief
Humility: You're willing to be proven wrong and change your mind based on evidence
Community engagement: You stay connected with other believers even while wrestling with questions
Time-bound searching: You're working toward resolution, not endlessly deconstructing
Honest doubt is actually a sign of intellectual and spiritual maturity. It means you're taking your faith seriously enough to examine it critically. You're refusing to believe something just because someone told you to believe it.
Cynical Doubt: The Skeptic's Conclusion
Cynical doubt, on the other hand, says, "I've already decided this isn't true, and nothing will change my mind." It's characterized by:
Closed-mindedness: No amount of evidence would satisfy because the conclusion is predetermined
Isolation: Withdrawing from community and from God
Performative questioning: Asking questions not to find answers but to appear intellectual or justify walking away
Endless deconstruction: Taking apart faith with no intention of rebuilding
The difference isn't in the questions themselves—it's in the heart behind them and the direction they're leading you.
Biblical Examples of Holy Doubt
Thomas isn't alone in his struggle with uncertainty. Scripture is filled with examples of faithful people who questioned, wrestled, and even argued with God.
Job: Questioning God's Justice
Job, described as "blameless and upright" (Job 1:1), spent 35 chapters demanding answers from God about his suffering. He didn't quietly accept his pain—he boldly challenged God's justice. And God's response? He engaged with Job. He showed up. He answered (though not in the way Job expected).
David: Wrestling in the Psalms
David, the man after God's own heart, wrote repeatedly about feeling abandoned by God:
"How long, O Lord? Will you forget me forever? How long will you hide your face from me?" (Psalm 13:1)
These weren't private thoughts David kept hidden. They became part of the inspired Scripture that millions of believers would read for encouragement. God apparently thought David's honest wrestling was worth preserving for all time.
The Father in Mark 9: The Most Honest Prayer
Perhaps the most relatable moment comes from a desperate father seeking healing for his demon-possessed son. When Jesus tells him, "All things are possible for one who believes," the father doesn't pretend to have rock-solid faith. Instead, he cries out:
"I believe; help my unbelief!" (Mark 9:24)
This is the prayer of honest doubt. "I believe... but I'm also struggling to believe. Help me." And Jesus heals his son.
Why Faith Without Questions Is Fragile Faith
Here's something most churches won't tell you: faith that's never been tested is faith that hasn't matured. Blind acceptance isn't a virtue—it's intellectual laziness masquerading as spirituality.
The Problem with Untested Faith
When you're taught that questions are dangerous, you develop a faith that can't withstand real-world challenges. The first time you encounter suffering that doesn't make sense, or prayers that seem unanswered, or theological problems you can't easily resolve, your entire belief system can collapse.
It's like building a house without ever checking if the foundation is solid. The moment a storm comes, everything crumbles.
The Strength of Examined Faith
But when you've wrestled with the hard questions and found that Christianity can actually stand up to scrutiny, you develop a resilient faith. You've tested the foundation and found it solid. You know why you believe what you believe.
This is why honest doubt can actually strengthen faith rather than destroy it. The questions force you to dig deeper, to search Scripture more carefully, to think more rigorously about what you believe and why.
Practical Framework: How to Doubt Well
If you're in a season of questioning, here's a practical framework for navigating it in a way that leads to growth rather than destruction:
1. Stay Connected to Community
This is absolutely critical. Isolation is where doubt turns toxic. When Thomas had his questions, he didn't leave the disciples—he stayed with them even though he couldn't believe what they believed.
Find a church or small group where honest questions are welcomed, not condemned. If your current community treats doubt as sin, you might need to find a healthier spiritual environment.
2. Keep Engaging with Scripture
Even if the Bible feels dry or confusing right now, keep reading it. Don't expect every reading to give you profound insights. Sometimes you're just showing up and being faithful to the process.
Think of it like physical exercise. You don't always feel like working out, and not every workout feels amazing. But consistency matters more than intensity.
3. Pray Honest Prayers
Stop trying to pray "correctly" and just talk to God like you'd talk to a friend. Tell Him about your doubts. Express your frustrations. Ask your hard questions out loud.
God isn't intimidated by your honesty. He already knows what you're thinking anyway. The honest prayer is always better than the pretend prayer.
4. Seek Wisdom from Multiple Sources
Read books by thoughtful Christians who have wrestled with similar questions. Not every doubt you have is unique—millions of believers throughout history have asked the same things and found satisfying answers.
Some recommendations:
"The Reason for God" by Tim Keller (addresses intellectual objections)
"Disappointment with God" by Philip Yancey (addresses emotional struggles)
"Mere Christianity" by C.S. Lewis (foundational apologetics)
5. Give Yourself Permission to Not Have All the Answers
You don't need to resolve every theological question before you can follow Jesus. Some questions won't have clear answers this side of eternity. And that's okay.
Faith isn't the absence of questions—it's trusting God even when some questions remain unanswered.
6. Look for Evidence in Changed Lives
While you're wrestling with intellectual questions, pay attention to the practical fruit of Christianity in people's lives. Do you see genuine transformation? Real love? Authentic community? Lives changed by grace?
Sometimes the best apologetic for Christianity isn't a philosophical argument—it's seeing the power of the gospel actually work in real people.
The Difference Between Seeking and Hiding
There's an important distinction between bringing your doubts to Jesus and using your doubts as an excuse to avoid Him.
Thomas stayed with the disciples. He didn't isolate himself. He didn't walk away from community because his questions made him uncomfortable. He remained present and engaged, even in his uncertainty.
That's seeking. That's honest doubt.
Hiding looks different. It's using your questions as justification for no longer reading Scripture, no longer praying, no longer participating in Christian community. It's treating doubt as a permanent state rather than a temporary season.
If you're truly seeking, you'll keep showing up even when it's hard. You'll stay engaged even when you're not sure. You'll keep asking, keep knocking, keep searching—because you actually want to find answers.
What to Do When Doubt Becomes Overwhelming
Sometimes doubt isn't just intellectual—it's emotional and spiritual. If you're in a place where you can barely pray, where reading the Bible feels impossible, where you're questioning everything, here's what you need to know:
You're Not Alone
Church history is full of saints who went through "dark nights of the soul"—seasons where God felt absent and faith felt impossible. Mother Teresa famously struggled with feelings of God's absence for decades. C.S. Lewis wrote about his devastation after his wife's death in "A Grief Observed."
Your struggle doesn't disqualify you. It makes you human.
Sometimes You Need Professional Help
If your doubt is tangled up with depression, anxiety, trauma, or grief, please consider seeing a Christian counselor or therapist. Mental health struggles can manifest as spiritual struggles, and sometimes you need professional support to work through both.
There's no shame in getting help. Taking care of your mental health is part of taking care of your spiritual health.
Let Others Carry Your Faith for a While
There are seasons where you might need to borrow faith from your community. When you can't pray, let others pray for you. When you can't believe, let others believe for you until you can believe again.
This is exactly what the Body of Christ is for—carrying each other when we can't carry ourselves.
The Long-Term View: Thomas's Legacy
Here's something powerful to remember: Thomas, the disciple we remember for his doubt, went on to become one of the most fearless missionaries in early Christianity. According to church tradition, he took the gospel all the way to India, where he was eventually martyred for his faith.
The doubter became the missionary. The questioner became the martyr.
His questions didn't disqualify him from ministry—they prepared him for it. Because when he finally encountered the risen Jesus, his faith wasn't based on blind acceptance. It was based on personal investigation and firsthand evidence.
That's the kind of faith that can withstand persecution. That's the kind of faith that can take you to the ends of the earth.
Your questions aren't disqualifying you. They might just be preparing you for something bigger than you can imagine right now.
The Invitation to Honest Faith
If you take away one thing from this post, let it be this: Jesus can handle your questions. He really can.
The problem isn't doubt—it's pretending we don't have doubts. It's performing faith when we're actually struggling. It's isolating ourselves because we think our questions make us bad Christians.
God isn't afraid of your honesty. He isn't intimidated by your struggles. He isn't waiting for you to get your theology perfect before He'll accept you.
He's inviting you to come exactly as you are—questions, doubts, confusion, and all. He's offering to meet you where you are, just like He met Thomas. He's saying, "You need evidence? Here it is. You need to understand? I'll help you. You need time? I'm patient."
The strongest faith isn't the faith that never questions. It's the faith that questions well—that brings its doubts to Jesus and waits for Him to show up.
And He always does. Maybe not in eight days like Thomas. Maybe not in the way you expect. But He shows up for honest doubters. Every single time.
So if you're in a season of doubt, don't run from it. Don't run from God. Run to Him with it. Stay in community. Keep reading. Keep praying, even if it's just "I believe; help my unbelief."
Your questions might just be the beginning of the deepest faith you've ever known.
What questions about faith have you been afraid to ask? Share them in the comments—let's create a safe space to doubt well together.
An Invitation to go Deeper….
If today’s message spoke to you, join the FaithLabz 30-Day Prayer Challenge and strengthen your connection with God’s unshakable love. You are never alone—let’s grow together!
