If there are only two Persons in the Godhead (the Father and the Son), how can one be baptized in the name of the Father, the Son, and the Holy Spirit?
Jesus said to His disciples, “All authority has been given to Me in heaven and in earth. Go therefore and make disciples of all the nations, baptizing them in the name of the Father and of the Son and of the Holy Spirit, teaching them to observe all things that I have commanded you; and lo, I am with you always, even to the end of the age” (Matthew 28:19,20).
The expression “in [eis, “into”] the name of” denotes “in recognition of the authority of (sometimes combined with the thought of relying or resting on)” (W. E. Vine, An Expository Dictionary of New Testament Words, p. 772). Baptism is performed in recognition of the Father’s authority, which is administered through the mediatorship of the Son and confirmed by the reception of the Holy Spirit.
The fact that the Father, Son, and Holy Spirit are mentioned together does not prove that all three are in precisely the same category. Paul speaks of “God and the Lord Jesus Christ and the elect angels” (1 Timothy 5:21), and no one would argue that the angels belong to the same category as God the Father and Christ the Son. Similarly, the fact that the Holy Spirit is mentioned along with the Father and the Son does not mean that the Spirit is the third Person of a triune Godhead.
Since the expression Holy Spirit is consistently used in reference to the presence and power of the transcendent God in the natural world, it is not surprising that Jesus Christ, who has been given authority in heaven and earth (the natural and supernatural worlds), should mention the Holy Spirit in this context. In heaven, the Father gives power to the Son. On earth, the expression of that power is called the “Holy Spirit,” “Spirit of God,” or “Spirit of Christ” (Romans 8:9–11). It is the presence and power of God, both the Father and the Son.