One difference between them is baptism. John says, "I baptize with water but the Messiah will baptize with the Holy Spirit and fire." He then adds that the Messiah will have a winnowing fork in his hand so that he can separate the wheat from the chaff. The chaff will be burned.
Fred Craddock in Preaching through the Christian Year C reminds us not to get preoccupied with the image of chaff burning:
"Spirit and fire" can also mean "wind and fire," which were symbol not only for the Holy Spirit (Acts 2:1-4) but for judgment as well. In fact, the present context seems to give this meaning to the baptism....One should not get preoccupied with the burning of chaff. The primary purpose is to save the grain.We can read this as good news if we consider that the parts of us that are sinful need to be eliminated so that we can be wheat gathered into God's granary.