Honest questions are rarely wrong, but the tone and the timing can be. God welcomed sincere questions from His servants when they were born out of a desire to please Him (Luke 1:34–38; Judges 6:12–18). So the answer to this question depends upon what is meant by “questioning the Bible.”
If “questioning the Bible” means that when we read something that seems implausible or contradictory we start asking questions, then that can be a healthy response. When we approach the Bible as God’s infallible Word, delivered through the hands of His trusted servants (2 Peter 1:21), we are pressed to wrestle through those questions because of a desire to know God better. God’s nature and ways are far beyond human comprehension. The Bible is God’s revelation to us about Himself and His interactions with humanity. But a book cannot contain all that He is. The Bible shows us as much of God as we are able to comprehend. So when students of the Bible come to passages or words that provoke questions, we either persevere until we have the answer or we finally say, “Lord, this doesn’t seem right to me, but you are God. I’m not. I trust you to always do what is right, and, if I don’t understand this, it’s my failure, not yours.” In that sense, “questioning the Bible” is not wrong. In fact, it helps us learn and grow. Many Christians have found that when they stop demanding an answer, God reveals it to them.
However, usually “questioning the Bible” means that we believe we have found an irreconcilable error and, because of that, we refuse to give the Bible the respect it deserves. When questioning the Bible sets us in judgment of the Bible, it is wrong. For centuries, Satan has worked to discredit the Bible’s accuracy, reliability, and authority. He uses the same tactics he used on Eve in the Garden of Eden by hissing, “Did God really say . . . ?” (Genesis 3:1). We see this challenge at its strongest these days with the advancement of the LGBTQ agenda. There is a mighty push to declare homosexuality righteous, but this cannot be done with the Bible in its proper place of authority. Thus, men invent ways to get around God’s clear prohibition of homosexual activity (Genesis 19:1–13; Leviticus 18:22; 20:13; Romans 1:26–27; 1 Corinthians 6:9). They question the Bible’s authorship, specifically the apostle Paul, claiming that people did not understand homosexuality at that time. They assert that ancient civilizations were not as informed or enlightened as we are today, and therefore the Bible’s moral standards are outdated. Churches and denominations are crumbling under this attack, because, like the Jews in Jesus’ day, they “loved the praise of men more than the praise of God” (John 12:43).
Another area people question the Bible about is its relevance. Many professing Christians declare that they believe the Bible to be God’s Word, but, other than some comforting psalms, it is no longer relevant to our culture. Some claim to read and love the Bible, but their lifestyles indicate something else. “Times are different now,” they say. “God understands that the 21st century is more advanced and some of those commandments just don’t apply to us now.” It is true that certain select portions of Scripture were for the Jews only during a specific era, but God Himself has not changed (Malachi 3:6; Hebrews 13:8). His moral law has not changed (Ecclesiastes 3:14; Isaiah 46:9–11). God judged nations for the sins that some professing Christians now champion (Numbers 25:1–3; Deuteronomy 20:17–18; 1 Kings 14:24). It is not difficult for a sincere student of the Bible to differentiate between the ceremonial laws God gave to the Israelites and the moral law that He gave to everyone (Genesis 9:5–6). So the Bible is completely relevant for us and for every other culture and time period.
Questioning the Bible in order to learn more and deepen our understanding can be healthy. But questioning the Bible in defiance of God is a rebellion that leads to eternal darkness (Revelation 21:8). The Bible is God’s instruction book for His human creations. When we reject or challenge its authority or relevance, we are closing the door on the only sure source of wisdom (James 1:5; John 17:17).