With Us, Then Within Us: Understanding the Holy Spirit Across Scripture

A Study in Scripture, Discernment, and New Covenant Assurance

Opening Meditation: “I Will Not Leave You as Orphans”

When Jesus spoke the words, “I will not leave you as orphans” (John 14:18), He was not offering emotional comfort alone. He was announcing a covenant reality, one that had never existed before in the history of God’s people.

Many believers know the phrase. Fewer understand the depth of its meaning.

To understand the Holy Spirit rightly, we must read Scripture across covenants, not across opinions. We must allow the Word itself to show us what remained the same and what truly changed.

This study is not about defending a position. It is about seeing clearly.

One Holy Spirit—One God—One Unified Work

Before we trace Scripture, we must establish what Scripture itself makes plain.

There has never been more than one Holy Spirit.

The apostle Paul writes:

“There is one body and one Spirit, just as you were called in one hope of your calling; one Lord, one faith, one baptism; one God and Father of all, who is above all, and through all, and in you all.”
Ephesians 4:4–6 (NKJV)

Scripture does not present an “Old Covenant Spirit” and a “New Covenant Spirit.”
What Scripture presents is one Spirit operating under different covenant arrangements.

The distinction, therefore, is not who the Holy Spirit is, but how He relates to God’s people.

The Holy Spirit Under the Old Covenant: Present, Powerful, but Not Indwelling

The Holy Spirit is active throughout the Old Testament. He creates, empowers, instructs, restrains, and reveals. Yet His relationship to God’s people follows a clear pattern.

The Spirit Came Upon People

The Spirit came upon individuals for specific purposes, often related to leadership, prophecy, deliverance, or craftsmanship.

• Prophets spoke as the Spirit moved them:

“The Spirit of the LORD spoke by me, And His word was on my tongue.” 2 Samuel 23:2

• Judges were empowered to deliver Israel:

“The Spirit of the LORD came upon him, and he judged Israel.” Judges 3:10

• Kings received divine empowerment:

“Then Samuel took the horn of oil and anointed him… and the Spirit of the LORD came upon David from that day forward.” 1 Samuel 16:13

Yet Scripture also shows that the Spirit could depart:

“But the Spirit of the LORD departed from Saul.” 1 Samuel 16:14

This alone tells us something critical: the indwelling was not permanent.

David’s Prayer: A Window Into Old Covenant Reality

David’s prayer in Psalm 51 is one of the clearest windows into how the Spirit was experienced under the Old Covenant.

“Do not cast me away from Your presence, And do not take Your Holy Spirit from me.” Psalm 51:11 (NKJV)

This prayer is not ignorance. It is theology shaped by experience.

David knew the Spirit could be removed, not because God was cruel, but because sin had not yet been fully atoned for.

Luke’s Gospel: Old Covenant Experience on the Brink of Change

Although the Gospel of Luke is in the New Testament, the events of Luke chapters 1 and 2 occur before the cross, and therefore are still under the Old Covenant.

Luke’s language is precise and consistent.

• Elizabeth:

“Elizabeth was filled with the Holy Spirit.” Luke 1:41

• Zechariah:

“Now his father Zechariah was filled with the Holy Spirit, and prophesied.” Luke 1:67

• Simeon:

“And the Holy Spirit was upon him.” Luke 2:25

Notice what Luke does not say:

• He does not say the Spirit dwelt within them

• He does not say the Spirit was permanent

• He does not say this was true for all believers

Luke is recording the final season of the Old Covenant, just before the transition.

Jesus’ Promise: A Relationship Never Before Known

Jesus introduces something radically new.

“And I will pray the Father, and He will give you another Helper, that He may abide with you forever.” John 14:16 (NKJV)

That word, forever, changes everything.

Jesus continues:

“He dwells with you and will be in you.” John 14:17 (NKJV)

This is the clearest distinction Scripture gives us:

• With you: Old Covenant experience

• In you: New Covenant reality

Jesus is not redefining the Spirit. He is redefining access.

Why This Could Not Happen Yet

Scripture explains plainly why this indwelling had not yet occurred:

“But this He spoke concerning the Spirit, whom those believing in Him would receive; for the Holy Spirit was not yet given, because Jesus was not yet glorified.” John 7:39 (NKJV)

Until sin was fully dealt with, permanent indwelling was not possible. The barrier was not God’s willingness; it was humanity’s condition.

The Cross and Pentecost: From Temporary to Permanent

When Jesus declared:

“It is finished.” John 19:30

The work of atonement was complete.

At Pentecost, the Holy Spirit did not come temporarily.

“And they were all filled with the Holy Spirit.” Acts 2:4 (NKJV)

This filling was not a repeat of Luke 1–2.
It was the inauguration of the New Covenant reality.

The Holy Spirit Under the New Covenant: Indwelling and Assurance

Under the New Covenant, believers themselves become the dwelling place of God.

“Do you not know that your body is the temple of the Holy Spirit who is in you, whom you have from God?” 1 Corinthians 6:19 (NKJV)

Paul reinforces this truth repeatedly:

“Now if anyone does not have the Spirit of Christ, he is not His.” Romans 8:9

And again:

“You received the Spirit of adoption by whom we cry out, ‘Abba, Father.’” Romans 8:15

The Spirit does not come and go.
He seals, assures, teaches, and transforms.

New Covenant Confidence: Not Orphans, Not Visitors

The believer no longer lives in fear of abandonment.

“In whom also, having believed, you were sealed with the Holy Spirit of promise.” Ephesians 1:13

A seal is not temporary.

The Holy Spirit now dwells within all believers, not a select few.

Reflection Questions

• Have I ever prayed or lived as though God might withdraw from me?

• How does understanding the permanence of the Spirit reshape my prayer life?

• In what areas of my life do I still act as though God is distant rather than dwelling within?

Sit with these questions slowly. Let Scripture answer them.

A Prayer of Gratitude and Discernment

Father God,

Thank You for Your Word, which brings light where confusion once lived. Thank You for not leaving us as orphans, but for sending Your Spirit to dwell within us. Help us grow in discernment, not only to understand truth, but to live from it. Teach us to walk in obedience, humility, and confidence, knowing that You are present, faithful, and near. May Your Spirit continue to lead us into truth, to form Christ within us, and to glorify You in all things.

In Jesus’ name,
Amen.