If John the Baptist recognised Jesus at his baptism, why did he later ask whether Jesus was the one to come?

John’s question came many months later and in very different circumstances, and both accounts can be true. When he baptised Jesus, John was free and preaching to great crowds. When he sent his disciples, he was in Herod’s prison (Matthew 11:2; 14:3), where he would die. He had preached a Messiah whose “fan is in his hand”, who would gather the wheat and burn the chaff (Matthew 3:12). Now he heard of Jesus healing and preaching, but saw no judgment and no release for himself. It is not hard to see how a faithful man, suffering for his faithfulness, could be perplexed and need to hear from Jesus himself. Ellicott calls it a question ‘of impatience rather than doubt’.

Even so, John does not ask ‘Who is this man?’ but “Art thou he that should come”, using a phrase for the promised Messiah: he starts from his own earlier witness. Jesus did not rebuke him. He sent back word of what he was doing, in words drawn from Isaiah’s prophecies of the Messiah’s day (Isaiah 35:5–6; 61:1), added the gentle warning, “blessed is he, whosoever shall not be offended in me” (Matthew 11:6), and then praised John to the crowds as “more than a prophet” (11:9). Scripture often shows faithful people struggling in this way when they suffer, like Elijah under the juniper tree (1 Kings 19:4) and Jeremiah after a night in the stocks (Jeremiah 20:2–9). A question asked in prison does not undo what John had seen.

For his disciples’ sake

Many older commentators, Gill among them, held that John himself did not doubt but sent his disciples so that they might see and hear Jesus for themselves and follow him. That would fit John’s own words, “He must increase, but I must decrease” (John 3:30). Against it, Jesus’ reply is addressed to John: “Go and shew John again those things which ye do hear and see” (Matthew 11:4).

Christians differ on whether John himself was troubled or asked for his disciples’ sake. As Barnes says, it is not certainly known why John sent to Jesus.