When speaking of the temple of the Holy Spirit, is it our physical body or the church or both?
The reference to the temple of the Spirit appears in two places:
"Do you not know that you are the temple of God and that the
Spirit of God dwells in you?"
I Corinthians 3:16
"Or do you not know that your body is the temple of the Holy
Spirit who is in you, whom you have from God, and you are not your own?"
I Corinthians 6:19
In both verses, the context shows that an individual is being addressed. For example, in I Corinthians 3:17 we read, "If anyone defiles the temple of God, God will destroy him. For the temple of God is holy, which temple you are." Notice the threat that God will destroy him is a reference to an individual an not to a church.
In the context of I Corinthians 6:19, Paul is talking about sexual immorality starting with verse 15. He argues that such sin is a sin against the person committing the sin. It is true that the church is refered to as the body of Christ (Ephesians 1:22-23), but notice that in the second reference Paul states that your body is the temple, not that His body is the temple. In fact, if we start with verse 18, it becomes very clear. "Flee sexual immorality. Every sin that a man does is outside the body, but he who commits sexual immorality sins against his own body. Or do you not know that your body is the temple of the Holy Spirit who is in you, whom you have from God, and you are not your own? For you were bought at a price; therefore glorify God in your body and in your spirit, which are God's." (I Corinthians 6:18-20).
Hence, in the two references to the temple of the Spirit, both references refer to the individual Christian.