The church of God is not necessarily found in one human organization or denomination; it is a spiritual organism composed of individual true Christians, wherever they may be. Ephesians 1:22-23 declares that the church is Christ's body and that He is its Head, which describes the church's organization and function in the world spiritually. So it was in the first century, when the twelve apostles and Paul scattered across the earth, raising up congregations everywhere. Whether under Peter, Paul, John, or another apostle, the truly converted members were united in the spiritual body of Christ despite having little or no contact with one another and working within different organizations. Revelation 2-3 more than suggests that end-time members will likewise be scattered among at least seven churches, though whether these are real organizations or spiritual designations in the mind of God cannot be said for certain. To consider only one physical organization the only true church ignores biblical reality. Even so, larger church organizations exist in which true disciples gather. Membership in the body is marked by being led by God's Spirit (Romans 8:14) and by keeping all of God's commandments (John 14:15). Such members are called out by the Father (John 6:44), and He will put a sincere seeker on the path to contact the true church.

The true church is a spiritual organism, not a single corporate institution, so it still exists even though it is scattered after the collapse of the Worldwide Church of God. Jesus promised, "I will build My church" (singular), and "the gates of Hades shall not prevail against it" (Matthew 16:18). He also spoke of one flock and one shepherd (John 10:16). The Greek word ekklesia means an assembly of called-out ones, and in Scripture it never refers to a building or a service. Scripture describes the church as a Kingdom, a building whose members are its materials, Christ's body with living parts, and a Family. No one volunteers to join it, and no one finds it by private searching. God draws people (John 6:44), and they are added to it upon repentance, baptism, and receiving the Holy Spirit. The church is small and nearly invisible, yet it endures because eternal life resides in it. Its unity was never permanently held in one corporate body. Gentile congregations spread beyond Jerusalem, and by the seven churches of Revelation 2 and 3 they were a mixed lot. Christ still treated each as His own, however flawed, so the scattered condition is the more normal one for the church. Today the called-out ones are spread among various Church of God groups, and God judges them individually within each. Because the church is exclusive and sanctified, it risks a Pharisaic, holier-than-you pride, which destroys fellowship. Members must instead use fellowship where it is available to grow, remembering that their calling is God's work, not their own.

The church is a spiritual organism, since a Christian becomes part of Christ's Body upon receiving the Holy Spirit, and the Body is one though it has many members (I Corinthians 12:20). Independents lean on this principle to claim that a congregation of one changes nothing, but they stretch it to its limit and rarely mention the Bible's emphasis on brotherly love, fellowship, and strong relationships. The church is not only a spiritual organism. God intends believers to be active members of a physical body as well. Christ's words in Matthew 16:18 show He had a corporate body of human beings in mind, since ekklesia means an assembly of people and the church exists continuously as flesh-and-blood believers. The pattern of Genesis 2:18, 24 teaches that it is not good for man to be independent, and that the most is not produced in those who are alone. God is reproducing Himself, and He is a unit of more than one Person. Jesus prayed that His disciples be one as the Father and Son are one (John 17:11, 22), and the Kingdom, like a nation, is one though it has many members. Those with the Spirit are to fellowship and serve together regularly (Hebrews 10:25). Scattered sheep are not in the fold, and Christ has given shepherds to tend His flock. Lone sheep are easily picked off by predators, while safety, service, love, and strength are found within the fold. The independent must repent of his independence in order to glorify God, serve His people, and mature spiritually.