Praying the Word: When You Struggle with Doubt

On the surface, prayer seems simple. It’s talking to God. But in practice, we may have a lot of questions. Am I doing this right? Is there a “right” way to do it? What am I supposed to say? Are there things I shouldn’t pray about? Or maybe we feel pretty comfortable with praying, but we struggle with getting bored or losing focus. 

Whatever our struggles with prayer, Scripture can be helpful. As Donald Whitney explains, “Praying the Bible isn’t complicated. Read through a few verses of Scripture, pause at the end of each phrase or verse, and pray about what the words suggest to you.” (You can read more from Donald Whitney about how to pray Scripture in this article.)

In the Praying the Word series, we’ll take the idea of praying Scripture and make it practical by sharing a passage of Scripture, an example prayer, and some guided questions to help you make it your own. The example prayer might serve as a model, or you can use it as a prayer for yourself. As you give this a try, don’t worry if it feels awkward or you’re not sure what to say. Remember, the power of prayer doesn’t come from the words we say, but from the One who hears them. 

Example Scripture

John 20:24-28

[24] Now Thomas, one of the twelve, called the Twin, was not with them when Jesus came. 

[25] So the other disciples told him, “We have seen the Lord.” But he said to them, “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.”

[26] Eight days later, his disciples were inside again, and Thomas was with them. Although the doors were locked, Jesus came and stood among them and said, “Peace be with you.” 

[27] Then he said to Thomas, “Put your finger here, and see my hands; and put out your hand, and place it in my side. Do not disbelieve, but believe.” 

[28] Thomas answered him, “My Lord and my God!”

Lord, thank you for including this snapshot of Thomas in your holy Word. His experience is so relatable and your response to his doubts is so comforting as I battle my own. He had walked and talked with his Savior and heard eyewitness accounts of the resurrection from his friends, and yet, he still doubted. He struggled to believe in your power and presence, just as I do at times. I wrestle with the truthfulness of Scripture, your sovereignty over the tough circumstances I walk through, and your steadfast love and goodness in my life. Do you see these sacrifices I’m making as a mom? Are you really near and attentive to my prayers, able to help me through each day’s work? I feel like it’s so often all up to me—that you’re distant or detached from my struggles to discipline my kids, clean up messes, or navigate parenting decisions with my husband. I look at other moms, whose lives seem so much more put-together, and wonder, “Is God withholding good from me?” Thank you that, in all these questions and more, I can express honest doubt and humble belief as you reveal yourself through your Word.

I praise you for the reminder that with your presence comes peace. You stood among your disciples, including doubting Thomas, and proclaimed the rest that I, too, long to have: “Peace be with you.” You answered Thomas’ questions and disbelief by actively showing up and letting him see your truthfulness face to face. Thank you that, in the middle of my questions and disbelief, you minister your presence and truth to me as well through your holy Word. As I take my concerns and fears to you today, deepen my faith. Open my eyes to see how you are providing for me in the midst of my responsibilities.

Thank you, Lord, that you are so gracious and merciful to those who doubt. You don’t chide Thomas for his unbelief—even considering all that he had seen you do in his life—but you tenderly call him back to faith. You hold out the proof of your resurrection and invite him to see and know it for himself. Help me likewise to respond to your call to “not disbelieve, but believe.” Give me the eyes of faith to take you at your Word and trust all of your promises—that you alone are God, you are in control of all things, and you love me with an everlasting love.

As I pour out my honest questions and you meet me in them, I pray that my heart would echo Thomas’s praise. Help me to see your greatness and glory, your power and perfection, in new ways and to worshipfully declare, “My Lord and my God!” Deepen my joy in you as you rekindle my belief in all that you are and have done. May I go forth delighting in you and boldly witnessing to other doubters that you are real, and you are near.

Make it Your Own

Praise God: What things in this Scripture passage give you reasons to praise God and thank him for who he is and what he’s doing? Give him both general and specific thanksgiving and come into his presence rejoicing.

Confess: What things do you need to tell God about how your heart or actions might veer (intentionally or unintentionally) toward self-reliance or even disobedience? Where have you trusted in your own wisdom or resisted his presence, commands, and care?

Share Your Heart: What things do you need to tell the Lord from a place of concern and humility? What questions linger, what worries do you harbor, and what do you need to hand over to him?

Ask: Where do you need wisdom? What help and grace do you need? Let the Lord know where you are weak and what specific things you need, letting him have the final and perfect say in how those needs are met and prayers are answered.


Annie VanderHeiden

Annie VanderHeiden serves as the Editor at Risen Motherhood and plants her roots in the uppermost corner of the PNW, enjoying salty sea air, mountain majesties, drizzly days, and mugs of matcha alongside her husband and two children. Annie’s first book, exploring Christ’s care for postpartum moms, releases in 2026 from P&R Publishing. Connect with her on Instagram.

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Mine: Why Balancing Motherhood and Self is Not the Answer