Thankfully, we can read the words John recorded and understand what Jesus was saying in context. Jesus is comparing himself to the manna that fell from heaven saying that he is the spiritual bread from heaven.
He ends the discourse explaining that he is speaking about the spirit not the flesh.
John 6
60 Therefore many of His disciples, when they heard this said, “This is a difficult statement; who can listen to it?” 61 But Jesus, conscious that His disciples grumbled at this, said to them, “Does this cause you to stumble? 62 What then if you see the Son of Man ascending to where He was before? 63 It is the Spirit who gives life; the flesh profits nothing; the words that I have spoken to you are spirit and are life.
The Alter-Christ claims that the physical body of Jesus gives life, Jesus said it profits nothing. Who should I believe, Jesus or the Alter-Christ?
There are two meanings to flesh in this part of scripture. Flesh equals Human. As in Human thinking not Spiritual thinking which is Above Human. God's way not Human way.
Ver. 64. The flesh profiteth nothing. Dead flesh, separated from the spirit, in the gross manner they supposed they were to eat his flesh, would profit nothing. Neither doth man's flesh, that is to say, man's natural and carnal apprehension, (which refuses to be subject to the spirit, and words of Christ) profit any thing.
But it would be the height of blasphemy, to say the living flesh of Christ (which we receive in the blessed sacrament, with his spirit, that is, with his soul and divinity) profiteth nothing. For if Christ's flesh had profited us nothing, he would never have taken flesh for us, nor died in the flesh for us. --- Are spirit and life. By proposing to you a heavenly sacrament, in which you shall receive, in a wonderful manner, spirit, grace and life. These words sufficiently correct the gross and carnal imagination of these Capharnaites, that he meant to give them his body and blood to eat in a visible and bloody manner, as flesh, says St. Augustine, is sold in the market, and in the shambles;[3] but they do not imply a figurative or metaphorical presence only.
The manner of Christ's presence is spiritual and under the outward appearances of bread and wine; but yet he is there truly and really present, by a change of the substance of bread and wine into the substance of his body and blood, which truly and really become our spiritual food, and are truly and really received in the holy sacrament.
--- The flesh[4] of itself profiteth nothing, not even the flesh of our Saviour Christ, were it not united to the divine person of Christ. But we must take care how we understand these words spoken by our Saviour: for it is certain, says St. Augustine, that the word made flesh, is the cause of all our happiness. (Witham) --- When I promise you life if you eat my flesh, I do not wish you to understand this of that gross and carnal manner, of cutting my members in pieces: such ideas are far from my mind: the flesh profiteth nothing. In the Scriptures, the word flesh is often put for the carnal manner of understanding any thing.
If you wish to enter into the spirit of my words, raise your hearts to a more elevated and spiritual way of understanding them. (Calmet) --- The reader may consult Des Mahis, p. 165, a convert from Protestantism, and who has proved the Catholic doctrine on the Eucharist in the most satisfactory manner, from the written word. Where he shows that Jesus Christ, speaking of his own body, never says the flesh, but my flesh: the former mode of expression is used to signify, as we have observed above, a carnal manner of understanding any thing.
From Haydock's commentary