43 The next day Jesus decided to go to Galilee. He found Philip and said to him, “Follow me.” 44 Now Philip was from Bethsaida, the city of Andrew and Peter. 45 Philip found Nathanael and said to him, “We have found him of whom Moses in the Law and also the prophets wrote, Jesus of Nazareth, the son of Joseph.” 46 Nathanael said to him, “Can anything good come out of Nazareth?” Philip said to him, “Come and see.” 47 Jesus saw Nathanael coming toward him and said of him, “Behold, an Israelite indeed, in whom there is no deceit!” 48 Nathanael said to him, “How do you know me?” Jesus answered him, “Before Philip called you, when you were under the fig tree, I saw you.” 49 Nathanael answered him, “Rabbi, you are the Son of God! You are the King of Israel!” 50 Jesus answered him, “Because I said to you, ‘I saw you under the fig tree,’ do you believe? You will see greater things than these.” 51 And he said to him, “Truly, truly, I say to you, you will see heaven opened, and the angels of God ascending and descending on the Son of Man.” (John 1:43-51)
“Before Philip called you, when you were under the fig tree I saw you.” This is all the prompting Nathanael needs to declare that Jesus is the Son of God and the King of Israel. It isn’t until much later that Peter calls Jesus the Christ, the Son of the Living God. Nathanael though, is convinced early on, by the testimony of John the Baptist, and his brother. And the fact that Jesus knows him and saw him under the fig tree, that is Jesus saw him praying. Nathanael understands that this must have been a vision that Jesus received. Nathanael had not spoken to anyone when he was under the fig tree, but to God. He was praying, the fig tree being the equivalent of a closet. It was a way of finding seclusion to be alone with your thoughts and prayers.
So the disciples, according to John, knew early on that Jesus was the Christ, but in the synoptics this confession comes much later. Some might try to pit the two against each other but this would be unwise. John the Baptist did indeed point out Jesus as the Messiah, the Christ, and the disciples believe him. But it is only later that this belief is filled with content as the disciples come to know Jesus. So it is with every Christian. Our faith grows as we study God’s word, and partake of the sacraments, vague notions are sometimes discarded and at other times given form.