Question:

Why did John question Jesus about who he was if he already knew? I am
talking about what he said about Jesus when he was in prison.

Answer:

This is a good question. I have thought about this often and not come up
with a completely satisfactory answer. Some people say that John was
doubting and that he really was unsure. It appears that you do not agree
with this interpretation. I am inclined to agree with you. John the
Baptist was well aware from all the way back at the time he baptized Jesus
(Matthew 3:13-17, John 1:26-27).

Let me share my speculation as to what was going on. Bear in mind that
this is somewhat of a guess. I believe that John the Baptist was well
aware that Jesus was the Messiah. It is my opinion that John was testing
the faith of this own followers. He hoped that they would hear the truth
from Jesus or his followers and be made to believe. Perhaps John was
using this as an opportunity to help some of his followers move into the
camp of Jesus, as he was well aware that his ministry was coming to an
end. This apparent moment of doubt was not the doubt of John the Baptist,
but of his believers. He used the opportunity to shore up their faith in
the one “the thongs of whose sandals I am not worthy to untie.” to use
John’s own words.

John Oakes, PhD