The Bible says that God’s eyes are too pure to look upon sin. So then how can the Holy Spirit be present at all times with people (even believers, who still commit sins)?

The verse does say something like that, and read as a doctrinal definition it creates a real contradiction. The first thing to notice is who is speaking, and why.

1. It is Habakkuk talking, not God. “You who are of purer eyes than to see evil and cannot look at wrong” (Habakkuk 1:13) is a line from the prophet's complaint, not a divine self-description. The book is a dialogue of protest, and the answer comes in chapter 2: “the righteous shall live by his faith.” Quoting chapter 1 as though it were God's own definition mistakes the question for the answer.

2. The context is outrage, not doctrine. Habakkuk is appalled that God would use the Babylonians — “that bitter and hasty nation” (Habakkuk 1:6) — to judge Judah. His line about pure eyes sets up the next clause: “why do you idly look at traitors and remain silent when the wicked swallows up the man more righteous than he?” It is a protest, and it is the setup for an answer he has not heard yet.

3. “Cannot look” means “cannot approve”. Hebrew sight language regularly carries the sense of regard or favor: God “saw” the light and called it good (Genesis 1:4); he “looks on the humble” (Psalm 138:6). To refuse to look on evil is to refuse to countenance it. The idiom is about approval, not eyesight.

4. Scripture says God sees everything. “The eyes of the Lord are in every place, keeping watch on the evil and the good” (Proverbs 15:3). “No creature is hidden from his sight, but all are naked and exposed to the eyes of him to whom we must give account” (Hebrews 4:13). Whatever Habakkuk meant, he cannot have meant that God is unaware of sin.

5. Presence is not endorsement. “Where shall I go from your Spirit? Or where shall I flee from your presence?” (Psalm 139:7-8). Being in the same room as a sin is not consenting to it. Omnipresence and approval are different categories, and collapsing them is the mistake the objection makes at its first step.

6. Jesus is the test case. He touched lepers, ate with tax collectors and sinners (Mark 2:15-17), and let a woman wash his feet with her tears — and the text insists he was without sin (Hebrews 4:15). His holiness was not endangered by contact; the contact was healing. If proximity to sinners were defilement, the incarnation is incoherent.

7. The Spirit's presence is what convicts. He “will convict the world concerning sin and righteousness and judgment” (John 16:8), and confession follows (1 John 1:8-9). A resident Spirit is not divine indulgence; he is the mechanism of ongoing repentance. The presence the objection treats as laxity is the thing that makes change possible.

8. The cross is where the tension resolves. God is “just and the justifier of the one who has faith in Jesus” (Romans 3:25-26) because Christ bore the sin he cannot approve: “For our sake he made him to be sin who knew no sin” (2 Corinthians 5:21). He does not overlook sin in order to be near sinners. He deals with it, and draws near on that basis.

9. The objection needs the holiness it mocks. If God's purity were indifference, his presence with sinners would be unremarkable and grace would mean nothing — there would be nothing to forgive and nothing to be saved from. The complaint only has force because holiness matters, which is the doctrine being denied. It borrows the Christian premise to attack the Christian conclusion.

The verse is a prophet's anguished question, and the book answers it. What looks like a contradiction is an idiom plus a category mistake: God sees sin perfectly, refuses to approve it, and comes near to sinners in order to deal with it.

Sources: Norman Geisler & Thomas Howe, Big Book of Bible Difficulties; D.A. Carson; O. Palmer Robertson, The Books of Nahum, Habakkuk, and Zephaniah.

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