Why is it so important to point out that John 6 doesn’t refer to the Lord’s Supper? – It is primarily a matter of biblical interpretation. The important Reformation principle of sola scriptura [the Scriptures alone interprets the Scriptures] demands that every doctrine of the church be drawn only from passages that speak of that doctrine. To draw a doctrine from passages of Scripture which speak of a different subject would mean reading theology into Scripture instead of drawing theology from the Scripture.
There are several things in the discourse itself that show that Jesus does not seem to be speaking of the Lord’s Supper in John 6. First of all, consider the context. [A text without a context becomes a pretext for something else!] Jesus has just fed the five thousand (John 6:1-15) who have now followed him to the other side of the Sea of Galilee, hoping that Jesus will feed them miraculously again. But Jesus turns their minds from earthly food to the more important matter of having a right relationship with God (cf. John 6:27-29; note how the people’s response to Jesus’ words shows their understanding of his figurative language).
The principle of sola scriptura urges us to draw doctrine from Scripture passages that clearly speak of that doctrine. Since John 6 is about the necessity of believing in Jesus as the Savior, it does not appear wise to turn there to establish the doctrine of the Lord’s Supper. Instead, we draw our doctrine of the Supper from the words of institution recorded in the Matthew, Mark, and Luke, and to Paul’s words concerning the Supper in 1Corinthians. By following this important principle of biblical interpretation, we protect ourselves from saying less and from saying more than Scripture.
Notice also the care with which Jesus chooses his terms in this discussion. Throughout the chapter, Jesus always refers to his “flesh” (Greek: sarx) rather than his “body” (Greek: soma). It would seem strange – if Jesus wants us to understand the eating and drinking here to refer to the Lord’s Supper – that he would use a different word than the one he used in the upper room and with Paul.
Many who insist that John 6 is speaking of the Lord’s Supper deny the real presence. They insist Jesus’ figurative words must refer to the Lord’s Supper and, therefore, his body and blood are only figuratively or spiritually present in the Lord’s Supper.
It is difficult if not impossible for any New Testament Christian to read John 6 without thinking of the Lord’s Supper. In addition to the oral reception of Christ's true body and blood in the Supper, we also know that there is a spiritual eating in the Supper which is identical with the spiritual eating of John 6. However, to insist that John 6 is about the Lord’s Supper (and therefore to seek to draw doctrinal truths about the Lord's Supper from John 6) seems not to deal fully with the context of the chapter.