What if I am Having Doubts? A Pastor’s Answer

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Jesus is Not Scared of Your Doubt.

I regularly answer questions about the faith from believers here, on social media, in person, and by email. The questions tend to repeat and deal with common issues. So I thought I would post some of them here and provide simple answers for those who don’t have a pastor or person to ask directly.

This one is simple. What if I have doubts about God? What do I do?

You are not unique as a Christian in having doubts. You are not alone in your questioning. I know this seems like the wrong message when discussing faith issues. But it is the truth. It is also comforting and encouraging. Why? We have all been where you are now. Even the most faithful Christian has dealt with challenges to their faith…just like you. They got through it and so can you.

You are an individual creation of the Most High God. You are also just a regular person. You naturally come with the same sins, doubts, fears, questions, and desires as every other human. The Bible says there is no temptation that is not common to man. This includes the one towards doubt..no matter how you were raised, how long you have been in church, and how much you experienced. Everyone who follows Christ will wrestle with faith questions at some point. It is what you do with it that matters.

Christians for 2,000 years have grappled with the exact same questions that plague you right now. It does not matter if they are related to science or attacks on biblical authority, other Christians have dealt with the same issues many times. They walked through the Valley of the Shadow of Doubt and came out loving Jesus even more on the other side.

They important thing is they did not deny their doubts. They admitted they had persistent questions. The then sought Jesus until they found answers. They took them to God and were satisfied. He always has the answers and is not afraid of questioning. They are often different than you expect.

Running from the Bible

Jepthah was my boogeyman when I first came to faith. I started off reading the Bible with excitement. I dived into this new wonderful world of God’s Word. It was going perfectly as I read the verses and stories that did not challenge me. Jesus saving sinners sounded great. God fighting for me even better. Then Jepthah and his daughter were thrown at me by an atheist co-worker. This skeptic claimed the Old Testament God is a monster and not at all like Jesus. I took up his challenge with much zeal and little wisdom and read Judges 11. I was shocked by what I found.


Jepthah was a Judge of Israel. He was not a great guy. The main issue I discovered is Jepthah is claimed to have sacrificed his daughter to God. Wait, what? I did not think they did this sort of thing in the Bible. They did not mention such things in the seeker sensitive mega-church I attended. “How could God include such a bad guy in the Bible?“, I thought. This is terrible! I then shut away Jepthah and his daughter as far from my thoughts as I could. Denial is not just a river in Africa! Not thinking about it would solve everything! The issue was I honest fear of the questions it raised for me. I was afraid of learning what my co-worker said was possibly true. This was one of my times of anxiety and doubt in my faith. My response was a huge mistake. Denial and avoidance help no one.

The high profile “deconversions” stories that flood the news seem to share this same error. The person leaving Christianity is usually raised in the church and taught about the Bible. They know all the stories of Noah, Abraham, and the Apostles. They have heard all of the inspirational sermons how the Bible can improve your life. They know Christian culture inside and out. Yet, it is all in a general sort of way with emphasis on them. Whether it be expressed in legalism or smushy “Be happy for Jesus” type doctrines, it is still focused on them. It is about the Christian rather than the Christ. This sort of faith naturally leads to serious doubts.

You never experience Christ while staring at yourself.

The “deconstructed” person may have been deeply involved in church culture. They might have even wrote books, led worship, or otherwise were influential. Yet, through it all they had persistent fear that God did not have all the answers. They swallowed these questions deep down inside until they walked away from the faith.

This is not the way it was meant to be with Jesus…for them or for me. Perfect love casts out all fear.

Years would pass before the Lord showed me His way to respond to my questions. It was through the Apostle who shares my name, Thomas.

Destroying the Doubt of Thomas

Thomas experienced Jesus personally. He saw most of the Lord’s ministry with his own eyes. He touched Lazarus after the grave clothes were removed. He ate of the multiplied fish and loaves. He heard Jesus say He will be crucified and everyone will abandon Him. Jesus told Thomas directly about the third day. It was, therefore, surprising he earned his nickname, “Doubting Thomas”.

Thomas should have expected Jesus’ resurrection. Jesus told him it would happen. Thomas could have been waiting at the Tomb. The problem was Thomas was human like you and I. He was subject to sin and doubts due to his own flesh. So when his closest companions tell Thomas they saw Jesus, what did he do? He doubted. He refused to believe. He went so far as declaring he would not believe it until touched Jesus side and hands and feet. He grabbed onto his skepticism and wrapped himself in it. He earned his nickname.

Have you felt this sort of doubt? Are you there now? Join the club. Many of the great names in Christian history were there before you. Billy Graham experienced a crisis of faith early in his ministry. He was a pastor speaking to thousands at a time. Yet, a dear friend’s deconstruction shook him to the core. He made it though. There is no shame in it. You just don’t have to stay there. Take it to Jesus!

Thomas set his mind on disbelief. Yet, he doesn’t stay there. He still shows up among the disciples. He voices his questions. He does not run from them. His focus is also where it should be – on Jesus. He demands answers from Jesus to help him understand and believe. This is a good example for Christians in the same situation. It is when Jesus shows up that things change.

It is really important to note Jesus’ response. How does Jesus respond to a very confused disciple?

Jesus does not stonewall doubt.


Jesus does not pretend there is no doubt.

Jesus does not scold the questioner.

Jesus does not call Thomas unworthy or unholy.

Jesus does not demand “blind faith”.

Jesus gives you mercy and grace in your time of need. Just like it says in the Bible:

Let us therefore come boldly to the throne of grace, that we may obtain mercy and find grace to help in time of need.

Jesus does not put out the smoking flax. God does not break the bruised reed. He tends to both and restores them to strength and health.

God Answers if You are Willing

Jesus invites the doubter to bring the questions directly to Him. Jesus is not offended by the questions. I would be if I just died for Thomas but that is why Jesus is Savior and I am not. Jesus does not need to explain Himself or prove the Resurrection to anyone. Yet, He lovingly gave Thomas exactly what he needs to get through his hard time. Jesus offered the holes in his hands and side to Thomas to allow him to overcome the temptation.

Thomas response is wonderful! He worships Jesus and says “My Lord and My God!” He walks away from Jesus full of faith and glorifying God.

Did you notice what Thomas did to earn this answer from Jesus?

What great act of obedience did Thomas perform to save his faith?

What was Thomas’ secret?

The answer is nothing. He did not do a thing to earn Jesus’ response. He had no secret. He was quite disobedient, stubborn, and rebellious, in fact. The wonderful truth about your relationship with Jesus is it is not about your good deeds, your faithfulness, and your love. It is all about Jesus’, thank God. His faith never wavers. His love doesn’t change. His mercy and grace is always freely given to you…even when you tell Jesus you have a hard time with Him. Thomas showed up with skepticism. He presented his own disbelief to God. Jesus loved him anyway. His presence changed Thomas’ entire perspective.

I returned to Jepthah and his daughter years after my first encounter. I still had questions but I was tired of running. I determined to bring them to Jesus just like Thomas. There was a difference this time. I went in armed with an arsenal of many Bible studies taught by mature believers, knowing Jesus, and learning the Bible. I learned the importance of context. I took all this and the questions directly to Jesus in prayer and in faith. Most importantly, I went in humbly understanding my feelings on the subject were likely just that…my feelings. They are often wrong. My feelings and conclusions never dictate to God. Jesus answered with mercy and grace.

You see, the entire point of the Book of Judges was not what I thought it was. The book is a warning and example of what happens when men go their own way and don’t listen to God. Judges is filled with bad actions by men and wayward men. Jepthah is one of them. There is a significant disagreement over whether Jepthah actually sacrifices his daughter. He may have sent her away to serve as a virgin in the Temple like a female version of Samuel. But what is very clear is God never asked Jepthah to do what he did. It was a foolish choice made by a flawed person in a book meant to highlight man’s helplessness without God.

Jepthah does not reflect poorly on God. Jepthah actually accurately testifies against man. The answer was clear. I just had to be willing to humble myself and admit my fears were wrong. I did not know everything and needed to ask God to teach me. This “bad man” was in the Bible to show what happens when man relies on his own judgment…kind of exactly like I did.

Jesus already knows you have doubts. He knows you are struggling. He is not angry or shaming you. He knows you are human. Now is the time to take them to the Throne of grace and work out your faith for you. Lean into it with an open mind and not following the influences of the world. Pray about it. Bring those doubts to Jesus and ask Him for answers. Get to know your Savior intimately and know His character.

Seek out the answers to the questions keeping you up at night. They are not new. Christians have worked through the same issues for 2,000 years now. There are Bible studies, apologetic resources, and loving believers available for you to learn from. There are loads and loads of answers if you are willing to hear. I would be blessed to talk about any Bible question or doubt you have in the comments or through email.

Jesus is not afraid of your questions. He is not intimidated by the gotcha questions of pop-atheists. He will not run from a hard question. But these do tend to tear apart your faith if they are allowed to fester unanswered. Bring it all to Jesus and be satisfied today.