Beyond Fear: How to Study the Bible When You Have Doubts

Let me tell you something that might surprise you: I’ve questioned the Bible. Not just difficult theological concepts or complex prophecies, but basic things. Simple stories that seemed to contradict each other. Historical details that didn’t line up. And in those moments, I felt like a pastor who had lost his faith—until I learned that questioning isn’t the opposite of faith; it’s often faith seeking understanding.

It happened during my second year of seminary. I was reading through Chronicles and Kings for a comparative study, and I stumbled across different numbers for the same census. My margin notes became increasingly frustrated. “This doesn’t add up,” I scribbled. “How can both accounts be true?” The questions multiplied faster than I could find answers. What started as academic curiosity became a crisis of confidence that kept me awake at night.

If you’ve ever felt that sinking feeling when Scripture raises more questions than answers, you’re in good company. Last week, we explored how familiar passages can feel stale and routine. But what happens when passages don’t feel familiar at all—when they feel foreign, confusing, or contradictory? When doubt creeps in and makes you wonder if you can trust anything you’re reading?

That uncomfortable space between faith and questions is where many Christians find themselves, yet few talk about it openly. We’re afraid that admitting doubt means we lack faith, when actually, it might mean our faith is mature enough to wrestle with hard things.

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The Hidden Struggle of Christian Doubt

Here’s what I’ve learned in years of pastoral ministry: doubt visits everyone in the church. It reaches brand-new believers and seasoned saints alike. The college student wrestling with science and Scripture sits in the same pew as the grandmother who’s begun questioning stories she’s believed for decades. The difference isn’t in who experiences doubt—it’s in who feels safe enough to acknowledge it.

When we talk about “difficult passages,” we’re usually dealing with one of three challenges: seeming contradictions (like the different accounts of Jesus’s genealogy), cultural instructions that feel foreign (like head coverings or dietary laws), or passages about God’s judgment that seem harsh to modern readers. Each type requires slightly different tools, but all can be approached with the same fundamental attitude: curiosity rather than fear.

The church hasn’t always been a safe place for honest questions. Too often, we’ve treated doubt like a spiritual disease that needs quick healing. We quote verses about not doubting and encourage people to “just have faith” without creating space for the very real intellectual struggles that come with believing an ancient text in a modern world.

Yet some of the most faithful people in Scripture were also the most honest questioners. Job didn’t just accept his suffering—he demanded an audience with God to ask “Why?” David didn’t just praise God in the Psalms—he accused Him of sleeping through his crises. Thomas didn’t just accept the resurrection reports—he declared, “Unless I see the nail marks in his hands and put my finger where the nails were, and put my hand into his side, I will not believe” (John 20:25). John the Baptist, despite baptizing Jesus and hearing God’s voice from heaven, later sent disciples to ask, “Are you the one who is to come, or should we expect someone else?” (Matthew 11:3).

Why Questions Strengthen Rather Than Threaten Faith

Here’s what strikes me about Jesus’s response to these doubters: He never rebuked anyone for having questions. Thomas got to touch the wounds. John the Baptist received evidence rather than condemnation. The disciples’ constant confusion was met with patient explanation rather than dismissal.

What Jesus did rebuke was willful unbelief—the determined rejection of evidence, the hardening of hearts against truth, the refusal to see what was right in front of them. But honest questions born from a desire to understand? Those He welcomed.

As pastor and author Colin S. Smith wisely noted, “Doubt is questioning what you believe. Unbelief is a determined refusal to believe. Doubt is a struggle faced by the believer.” The difference is crucial. When you doubt, you’re still engaging with faith. You’re wrestling with God, not running from Him.

Research from the Fuller Youth Institute confirms what many pastors observe: “over 70% of churchgoing high schoolers report having serious doubts about faith. Sadly, less than half of those young people shared their doubts and struggles with an adult or friend. Yet, these students’ opportunities to express and explore their doubts were actually correlated with greater faith maturity.”

The silence is the problem, not the doubt itself. When we suffer alone with our questions, they grow larger and more frightening in the darkness. But when we bring them into the light—through study, conversation, and prayer—they often become pathways to deeper understanding.

Your questions don’t disqualify your faith. They might actually be evidence of it. Only someone who cares deeply about truth would wrestle with difficult passages. Only someone who takes Scripture seriously would be bothered by seeming inconsistencies. Your discomfort with easy answers might be the Spirit’s way of driving you to deeper wells.

Two Approaches That Transform Doubt into Discovery

During my own season of wrestling with Scripture, I discovered two approaches that consistently helped me move from paralyzing doubt to productive study. These aren’t quick fixes—they’re ways of engaging with Scripture that honor both the text and your honest questions.

Study with Curiosity, Not Certainty

Let me show you how this works with a concrete example. Consider the seeming contradiction in Jesus’s genealogies. Matthew 1:16 says Joseph’s father was Jacob, while Luke 3:23 says Joseph’s father was Heli. At first glance, these seem completely incompatible—Joseph can’t have two different fathers.

But when you approach this with curiosity instead of defensiveness, different questions emerge: Could one genealogy trace the legal lineage while the other traces the biological line? Could these represent Joseph’s lineage versus Mary’s lineage? Could adoption or levirate marriage explain the difference? Suddenly, what seemed like a contradiction becomes evidence of the Gospels’ different purposes—Matthew emphasizing Jesus’s royal legal claim through Solomon, Luke emphasizing his priestly line through Nathan.

This process—moving from “this doesn’t make sense” to “help me understand the historical context”—transforms study from a threat to faith into a strengthening of it. When you discover that careful investigation often reveals the complexity of real historical situations rather than simple errors, your confidence in Scripture’s reliability grows rather than shrinks.

The key is asking different questions: “What was the author trying to communicate to his original audience?” “What did this mean in their historical context?” “How would the first readers have understood this?” These questions move you from judge to student, from defender to detective.

Read with Community, Not Isolation

The second approach that transformed my study was refusing to wrestle with difficult passages alone. Doubt grows in isolation but often shrinks in community. When I brought my questions about census numbers to my professor, he didn’t rebuke my doubts—he handed me three commentaries and said, “Let’s figure this out together.”

The Ethiopian eunuch in Acts 8 was reading Scripture when Philip approached him. “Do you understand what you’re reading?” Philip asked. The eunuch’s response is both humble and wise: “How can I, unless someone guides me?” (Acts 8:31).

Find people who can walk with you through the questions. This might be a pastor, a small group, a mentor, or even online communities of believers who take Scripture seriously. Look for people who don’t dismiss your doubts but also don’t let you camp in them indefinitely. The goal isn’t to eliminate all questions—it’s to learn how to hold questions and faith in the same hands.

Practical Steps for Studying When You Doubt

If you’re ready to move beyond the fear that often accompanies doubt, here are three practical steps you can take this week:

Start with a manageable challenging passage. Instead of tackling the most complex theological puzzles, begin with something like the different genealogies of Jesus (Matthew 1:16 vs. Luke 3:23) or the varying details in Gospel accounts. These have clear, discoverable explanations that will build your confidence for harder questions.

Find one trusted resource for historical context. Invest in a good study Bible with notes, a basic commentary, or access to online resources like Blue Letter Bible. Context resolves more difficulties than any other single tool. Understanding first-century culture, Jewish customs, or ancient historiography methods often makes puzzling passages suddenly clear.

Share one specific question with a trusted person. Don’t let your doubts fester in isolation. Choose someone—a pastor, mentor, small group leader, or mature Christian friend—and ask them about a passage that’s been troubling you. Often, you’ll discover you’re not the first person to wrestle with this question, and their perspective might provide exactly the insight you need.

When Wrestling Leads to Worship

Here’s the beautiful outcome I’ve witnessed repeatedly in my own life and in the lives of others who’ve learned to study Scripture through their doubts: wrestling often leads to worship. When you work through a difficult passage and finally understand what the author was communicating, when you see how seeming contradictions actually reveal the Bible’s authenticity, when you discover that your questions were leading you to deeper truth—something remarkable happens.

Your faith becomes your own. Not inherited, not handed down, not accepted without thought, but personally tested and proven. The Scripture that once raised questions becomes the Scripture that provides answers. The passages that made you doubt become the passages that strengthen your confidence in God’s Word.

This isn’t about intellectual pride or having all the answers. It’s about developing what I call “tested faith”—a confidence in Scripture that has been through the refining fire of honest questioning and emerged stronger. When someone challenges your beliefs, you’re not threatened because you’ve already wrestled with the hard questions yourself.

Your doubts don’t have to be the end of your faith story. They might be the beginning of the most authentic chapter yet. When you learn to study Scripture with your questions rather than despite them, you discover that God is not threatened by your intellectual honesty. He’s honored by it.

The same Lord who welcomed Thomas’s doubts and answered John’s questions is patient with yours. He’s not waiting for you to stop asking hard questions about His Word. He’s waiting for you to bring those questions directly to Him, confident that He who authored Scripture is more than capable of helping you understand it.

Beyond the fear of doubt lies the freedom to study with both faith and intellect fully engaged. That’s where real spiritual growth happens—not in the absence of questions, but in the courage to seek answers.

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