“Truly, truly, I say to you, he who believes has eternal life. I am the bread of life. Your fathers ate the manna in the wilderness, and they died. This is the bread which comes down from heaven, that a man may eat of it and not die. I am the living bread which came down from heaven; if any one eats of this bread, he will live for ever; and the bread which I shall give for the life of the world is my flesh.” The Jews then disputed among themselves, saying, “How can this man give us his flesh to eat?” So Jesus said to them, “Truly, truly, I say to you, unless you eat the flesh of the Son of man and drink his blood, you have no life in you; he who eats my flesh and drinks my blood has eternal life, and I will raise him up at the last day. For my flesh is food indeed, and my blood is drink indeed. He who eats my flesh and drinks my blood abides in me, and I in him. As the living Father sent me, and I live because of the Father, so he who eats me will live because of me. This is the bread which came down from heaven, not such as the fathers ate and died; he who eats this bread will live for ever.” (John 6:47-58)

Jesus is clear that he is referring to eating, not merely believing in him (which is also a necessity). First, he emphasizes belief and faith in him, and “coming” to him (6:29, 35-36, 40, 44-45, 47, and reiterated in 6:64-65). John 6:27, with its reference to “food” was a “preview,” so to speak, of what is to come.

Then in John 6:50-58 he starts speaking specifically about eating his flesh and not just believing in him, and mentions “eat[s]” seven times and “drink[s]” four times in eight verses where he is speaking, with 6:55 (above) also referring again to “food” — for a total of 12 references to eating and drinking in eight verses. This is why we believe it has a physical element as well as non-physical.

Additionally, he refers (as the referent of what we are to eat and drink) to his “flesh” five times, his “blood” four times, “bread” (referring to himself) six times, and “eats me” once (6:57). That’s 16 more references to eating (him) in these eight verses for a grand total of 28 references to eating and drinking his flesh and blood in eight verses (an average of 3.5 times per verse).

To remove all doubt, he equates the “living bread” with his “flesh” in 6:51. What more does one need to be persuaded, pray tell? It couldn’t have been made any more clear than it is.

Non-believers in transubstantiation will often claim that Jesus’ contrast of “flesh” and “spirit” in 6:63 establishes the symbolic and metaphorical nature of the whole discourse.

But when the words “flesh” and “spirit” are opposed to each other in the New Testament, it is always a figurative use, in the sense of sinful human nature (“flesh”) contrasted with humanity enriched by God’s grace (“spirit”). See Matthew 26:41; Romans 7:5-6, 25; 8:1-14; 1 Corinthians 5:5; Galatians 3:3; 4:29; 5:13-26; 1 Peter 18; 4:6.

In other words, Jesus is saying that his words can only be received by men endowed with supernatural grace. Those who interpret them in a wooden, carnal way — equating his teaching here with a sort of gross cannibalism — (or with a merely natural human understanding; see, e.g., Matthew 16:17 for an example of this meaning) are way off the mark.

He wasn’t referring to the Holy Eucharist, but rather to “the words that I have spoken.” “Spirit and life” refers back to his references to spiritual and eternal life as a result of partaking of the Eucharist (6:50-51, 53-54, 56-58).

In many other places in Scripture, Jesus explains his meaning when someone merely is uncomprehending (as opposed to willfully disbelieving). A typical example of this occurs in John 3:1-15 — the incident with Nicodemus regarding the meaning of “born again.” Nicodemus asks, “How can a man be born when he is old? Can he enter a second time into his mother’s womb and be born?” (3:4). Jesus explains his meaning (3:5-8).

Nicodemus, still baffled, again asks, “How can this be?” (3:9). Jesus replied: “Are you a teacher of Israel, and yet you do not understand this?” (3:10) and then proceeds to explain some more (3:11-15), because he knew that Nicodemus was truly seeking.

When someone wasn’t seeking or open in their spirit, he usually (if not always) would not do so, as in John 6 (see: Matthew 13:36, 51; 15:10-20; 16:5-12; 17:9-13; 19:24-26; Mark 4:33-34; Luke 8:9-15, 46-48; 24:13-27; John 4:31-34; 8:21-32.

But he didn’t explain his miracles. He never explained how he could walk on water or still the winds or be transfigured or know people’s private thoughts, or raise people from the dead. So why should he explain all the ins and outs of the Eucharist?

There are many odd and weird and unpredictable manifestations of God throughout the Bible. How can we be the Body of Christ (Romans 7:4; 1 Corinthians 12:27; Ephesians 1:22-23; 4:12; 5:30; Colossians 1:24)? When St. Paul was converted to Christ, Jesus said to him, “I am Jesus, whom you are persecuting” (Acts 9:5). 

This couldn’t literally refer to Jesus the Divine Person since he had already ascended to heaven (Acts 1:9-11). Rather, Jesus meant that Christ’s Church really was his Body, whom Paul (Saul) was persecuting (Acts 8:1, 3, 9:1-2).

What does Paul mean by “carrying in the body the death of Jesus” (2 Corinthians 4:10), or “in my flesh I complete what is lacking in Christ’s afflictions” (Colossians 1:24)? There is plenty of mystery to go around, and the Eucharist is by no means a unique case.