Just as I view John 3 as a teaching on the sacrament of Baptism, I view John 6 as a teaching on the sacrament of the Eucharist. Forms of the word eucharist appear earlier in John 6:11, 23, as forms of the word *baptism *appear in John 3:22,23,26. So, I view John 6:63 in the context of the sacrament of the Eucharist. However, I think the theme of John 6:63 actually applies to all the sacraments.
When Jesus says, “It is the spirit that gives life, the flesh is unprofitable,” I think he means, “It is the spirit that gives life; the flesh,* without the spirit*, is *spiritually *unprofitable.” In this case, “the spirit” refers to gifts of the Holy Spirit that are spiritually discerned, i.e., discerned by faith, as in 1 Corinthians 2:14. And, “the flesh” refers to things of the visible world, as in Romans 8:1-17.
The sacraments have a visible sign or “flesh” component and a corresponding, invisible, spiritually-significant action of the Holy Spirit. The visible sign or “flesh” component of the sacrament, without the corresponding action of the Holy Spirit, is spiritually unprofitable. For instance, the water bath of the sacrament of Baptism, apart from the spiritually-regenerating action of the Holy Spirit, is spiritually unprofitable and merely gets a person wet. Similarly, the bread and wine of sacrament of the Eucharist, apart from the transubstantiating action of the Holy Spirit whereby they are transubstantiated into the body and blood of Jesus, is spiritually unprofitable and merely affords a person a bit of bread and wine.