Did John the Baptist know Jesus was Messiah or not?

In John 1, John the Baptist is quoted as saying:

John 1:30 “This is He on behalf of whom I said, ‘After me comes a Man who has a higher rank than I, for He existed before me.’ 
John 1:31 “I did not recognize Him, but so that He might be manifested to Israel, I came baptizing in water.” 
John 1:32 John testified saying, “I have seen the Spirit descending as a dove out of heaven, and He remained upon Him. 
John 1:33 “I did not recognize Him, but He who sent me to baptize in water said to me, ‘He upon whom you see the Spirit descending and remaining upon Him, this is the One who baptizes in the Holy Spirit.’ 
John 1:34 “I myself have seen, and have testified that this is the Son of God.” 

Notice John the Baptist himself says that he did not recognize Jesus nor did he know Jesus’ identity as Messiah until after he saw the Spirit descending and remaining on Jesus following Jesus’ baptism. Based on John’s own testimony, we must conclude that he didn’t know Jesus’ identity as Messiah until after he had baptized Jesus.

On the other hand, in Matthew’s Gospel we read:

Matt. 3:13  Then Jesus  arrived from Galilee at the Jordan coming to John, to be baptized by him. 
Matt. 3:14 But John tried to prevent Him, saying, “I have need to be baptized by You, and do You come to me?” 
Matt. 3:15 But Jesus answering said to him, “Permit it at this time; for in this way it is fitting for us to fulfill all righteousness.” Then he  permitted Him. 
Matt. 3:16 After being baptized, Jesus came up immediately from the water; and behold, the heavens were opened, and he saw the Spirit of God descending as a dove and lighting on Him, 
Matt. 3:17 and behold, a voice out of the heavens said, “This is My beloved Son, in whom I am well-pleased.” 

Matthew’s account records that John the Baptist hesitated to baptize Jesus in the beginning because John recognized Jesus’ superior position. John said Jesus should baptize him instead, implying John knew Jesus was the Messiah. Is this a contradiction with John’s account?

No, there is no contradiction. First, notice that Matthew’s account never says specifically what John knew of Jesus’ identity. Matthew’s account only indicates that John had great respect for Jesus’ righteousness. John was baptizing for the forgiveness of sins, so when John says, “I have need to be baptized by you,” he was simply acknowledging Jesus’ superior position in terms of righteousness. This acknowledgement doesn’t necessarily mean John knew Jesus to be the Messiah prior to His baptism.

Remember, John and Jesus were cousins born six months apart and likely grew up together, so Jesus’ superior righteousness must have been evident to John. Therefore, as John stood in the wilderness calling sinners to receive a water baptism for the repentance of sins, surely he would have been surprised to see his righteous cousin coming to him for such a baptism. John understood that Jesus was far more righteous than he, which explains why John exclaimed that Jesus should baptism him instead. 

Nevertheless, Jesus insisted on receiving baptism from John, and thereafter the Spirit descended on Jesus leading John to understand why Jesus was so righteous. John came to understand that Jesus was Messiah! 

Therefore, John’s Gospel and Matthew’s Gospel agree. John the Baptist didn’t know Jesus was Messiah until after the baptism, yet before that time John saw Jesus as the more righteous between them. We can see John’s words in Matthew 3 to be a testimony to us that Jesus did, in fact, live a sinless life. 

Scripture quotations taken from the (NASB®) New American Standard Bible®, Copyright © 1995, 2020 by The Lockman Foundation. Used by permission. All rights reserved. www.lockman.org