The idea of the Holy Spirit having a dwelling is well established in Scripture. In the Old Testament, the Hebrew word “shekhinah” means dwelling or settling and culminates into this Jewish idea of “Divine Presence”. We can read of God’s (e.g. Holy Spirit’s) dwelling among the people of Israel first in the wilderness wanderings (Exodus 13:21-22) and again with the dedication of the permanent temple in Jerusalem by Solomon (2 Chronicles 7:1-3).

Notably, God’s Holy Spirit did not fill the temple built by Zerubbabel in the days following the return of the Babylonian captives. Nor do we have any record of God’s Divine Presence filling Herod’s temple in the first century. So where is the Holy Spirit dwelling today?

How Scripture answers "Where is the Holy Spirit dwelling today?"

The Holy Spirit is dwelling in every baptized believer.234791011131415 It is rather “matter-of-factly” stated in many places.3691011141516 It is also a critical fulfillment to an ever-present Bible theme of God’s desire and promise11 to be with His people.

God dwelt among His people during the wanderings (tabernacle) and Solomon (temple) years. However, during the captivity (no temple) and remnant years, He was absent but promised a day when He would return58. In the first century, Jesus alludes to this promise711, and we see the fulfillment of that promise on the Day of Pentecost4. From that point on, we see these very plain statements by New Testament writers about the Holy Spirit dwelling in believers23691011131415 – and by extension, His church112.

Answer built on scripture-blocks below

Applying 1 Corinthians 3:16-17 to this question...

Paul states that they, as a local church, are a temple of God in which the Holy Spirit dwells.

Applying 1 Corinthians 6:18-20 to this question...

Paul states that the Christian’s body is the temple (dwelling) of the Holy Spirit given by God, the Father.

Extra Context for this Application:

In this context, the “body” is the individual Christian’s body (not the “body” in terms of the church, Christ’s body).

Applying Acts 5:30-32 to this question...

Peter states that God has given the/His Holy Spirit to all who obey Him (believers).6915

Applying Acts 2:37-39 to this question...

Peter says that their [water] baptism is directly connected to them receiving the gift/promise of the Holy Spirit.

Applying Haggai 2:4-6 to this question...

God, through Haggai, assures the people that His Spirit is still in their midst. However, He promises a future glimpse of something even greater. The “Yet once more” statement is defined and interpreted for us by an inspired writer in Hebrews 12:26-29.

Extra Context for this Application:

The Haggai and Hebrews passages don’t explicitly speak to the dwelling of God’s Spirit. However, in Haggai, God’s encouragement and promise of the future were in response to their noting the absence of God’s glory (Spirit) in their temple rebuild. Likewise, with the Hebrews passage, we know of many other passages that connect the coming of God’s kingdom with His Spirit dwelling and God returning “in their midst”.

Applying 1 John 4:13-15 to this question...

God, the Father, dwells in us because “he has given us of his Spirit”.

Extra Context for this Application:

John makes the point throughout his letter, but one other explicit example is 3:24, “Whoever keeps his commandments abides in God, and God in him. And by this we know that he abides in us, by the Spirit whom he has given us.”

Applying John 3:3-5 to this question...

Jesus references the role of the Spirit in one’s entering the kingdom of God. It was one of two “born again” elements – water (baptism) being the second.

Applying Ezekiel 36:25-27 to this question...

God, through Ezekiel, promises a time (a “day“) when He will put His Spirit “within you.”

Extra Context for this Application:

This theme in many other places in Ezekiel, including 37:14 and 37:26-28, and in the last few chapters of the book. His contemporary Jeremiah also uses very similar language and identical thought (Jeremiah 31:33). Two differnt men…but importantly both prophets of God so the same author (God) and message. While Ezekiel’s words are never directly quoted/interpreted by inspired writers in the New Testament, Jeremiah’s are interpreted in Hebrews and applied to the 1st-century church.

Applying 1 Thessalonians 4:7-8 to this question...

God gave his Spirit to those who have responded to his call for holiness.

Applying Romans 8:9 to this question...

The “Spirit of God” (or “Spirit of Christ” or Holy Spirit) dwells in those who are “not in the flesh”.

Extra Context for this Application:

Paul goes on to conclude and restate his declaration that God gives life to their fleshly bodies “through his Spirit who dwells in you” (vs 11).

Applying John 7:37-39 to this question...

Jesus speaks about “rivers of living water” coming from the believer’s heart. John confirms for us that he was speaking about the Holy Spirit that all believers would receive when Jesus was to be “glorified” (eg His ascension into heaven).

Applying Ephesians 2:19-22 to this question...

The indwelling of the Spirit in each Christian forms the basis for “the household of God” (all saints) being a “holy temple” dwelling place for God.1

Applying Ephesians 3:16-17 to this question...

The Holy Spirit is in our “inner being” (and in that way, Christ dwells in our hearts).

Applying 1 John 4:4 to this question...

John is reminding Christians of what is in them using a pronoun, “he” [Holy Spirit implied].

Applying Galatians 4:6-7 to this question...

Jesus’ Spirit – the Holy Spirit – is in our hearts if we are sons of God.

Applying 2 Peter 1:3-4 to this question...

Peter acknowledges that Christians are those who have “become partakers of the divine nature”.349

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