If John the Baptist was sure that Jesus was a Messiah (Matt. 3:14), then why did he doubt him in the other place (Matt. 11:3)? Does that mean NT accounts have contradictions?


This question has troubled me in the past as well.  It seems surprising that John the Baptist was the prophesied “one crying in the wilderness” (Isaiah 40:3), that he was the “messenger who will prepare the way before me.” (Malachi 3:1),  that he was the one who prepared the way for Jesus, who told the crowd that he was the lamb of God who takes away the sin of the world (John 1:29), and that he was such an amazing prophet for God, yet, later on he seems to have doubted about Jesus.  I cannot blame you for wondering if this is a contradiction.  This is a reasonable question.
One thing I know for sure, and there is plenty of evidence for this, is that the Bible is inspired by God.  So, the conclusion that there is a contradiction seems quite unlikely to me.  When we propose a contradiction, we ought to give the Bible the benefit of the doubt, as there is so much evidence for its inspiration.  So, we should ask if there is a reasonable explanation for what we see in John the Baptist’s behavior.  The relevant passage is Matthew 11:1-3, in which John, while in prison, sent his disciples to ask Jesus of he is the one, or if they should expect another. Presumably, he is asking whether Jesus is the expected Messiah.  How could John, who played such a pivotal role in identifying Jesus as the Messiah in John 1:29-34 or even in Matthew 3:13-17 now doubt Jesus?
I have two possible explanations.  The first possibility is that in Matthew 11:1-3, John the Baptist is not in fact doubting Jesus, but is sending his disciples to check out for themselves.  He is not telling them, but inviting them to find out for themselves.  If this is the case, then John is not actually doubting if Jesus is the one, but it sending his disciples to Jesus.  Rather than sending them away, he is inviting them to see the ministry of Jesus for themselves, which is why he speaks ambiguously about Jesus in 11:3.  This was my conclusion when I was a younger Christian.  I still believe this might be the case.
The other possibility, which seems quite surprising, but should be considered, is that John the Baptist really did come to doubt his original conviction.  It is understandable that he would be struggling, as, in Matthew 11:1-3 he is now in prison, and will very likely lose his life.  Any of us might begin to doubt under the stress of such persecution.  John the Baptist, as great a spiritual man as he was, may have bent somewhat under the strain of his arrest and pending execution. Although I was convinced of the first explanation as a younger Christian, I lean slightly to the second explanation now.
One thing we can be sure of is that there is no real contradiction. It is worth remembering that Matthew wrote both Matt 3:13-17 and Matt 11:1-3.  Surely Matthew is aware of both, as he wrote both in his own gospel!  There is one person who definitely did not see John’s earlier and later behavior as a Bible contradiction, and that person is Matthew, the author of the gospel.  Whether the correct explanation of John’s surprising behavior in Matthew 11:1-3 is the first or the second proposal above, I cannot say with complete certainty.  You can think about this for yourself.  However, what you can be quite confident of is that the earlier faithful John and the later seemingly less faithful John is not an unresolvable contradiction.  In fact, if we believe Matthew, it is not a contradiction at all.
John Oakes

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