Why Did God Allow Difficult Passages in Scripture?

Question 1114.

Difficult Bible passages are something every serious reader eventually meets, genealogies that seem endless, prophecies that stay obscure, apparent tensions between accounts, and commands that jar against modern sensibilities, and the honest question worth asking is why a God who wanted to communicate clearly would give us a book containing so much that puzzles us.

I want to take this question seriously rather than brushing it aside with a pat answer, because how we handle difficult Bible passages says a great deal about whether our confidence in Scripture is resilient or simply fragile and easily shaken.

Acknowledging That Difficult Bible Passages Are Real

We should say plainly that difficult Bible passages are not a modern invention or a product of sceptical scholarship. Even the apostle Peter, writing about Paul’s letters, admitted they contained “some things that are hard to understand, which the ignorant and unstable twist to their own destruction” (2 Peter 3:16). The Ethiopian eunuch, reading Isaiah on his chariot, told Philip plainly, “How can I, unless someone guides me?” (Acts 8:31). Even Jesus’ own disciples, after hearing Him teach directly, still asked Him afterwards to explain His parables.

If inspired apostles, sincere seekers and the Lord’s own disciples all found parts of Scripture genuinely challenging, we should not be surprised or embarrassed when we do too. Struggling with a difficult passage is not evidence of weak faith. It is evidence of a text with real depth, given by a God whose thoughts are higher than ours.

Why God Allowed a Book With Real Difficulties

Why, then, do difficult Bible passages exist at all? One answer lies in the nature of communication itself. Scripture was written across roughly fifteen centuries, by dozens of authors, in three ancient languages, addressing specific historical circumstances that we, reading two or three thousand years later, no longer share firsthand. Some difficulty is simply the ordinary cost of God speaking into real history rather than delivering an abstract, timeless list of propositions detached from any human context.

A second answer is more deliberately pedagogical. Difficult Bible passages drive us to read carefully, to study rather than skim, to consult the wider counsel of Scripture rather than build doctrine on a single isolated verse, and to depend on the Holy Spirit’s illuminating work rather than our own cleverness. A text with no difficulty at all might invite laziness. A text with genuine depth invites the diligence Proverbs commends when it speaks of searching for wisdom as for hidden treasure.

Categories of Difficulty Worth Distinguishing

Not every difficult Bible passage is difficult for the same reason, and it helps to sort them into rough categories. Some difficulties are historical or cultural, requiring background knowledge about ancient customs we no longer share. Some are textual, involving genuine questions about the exact original wording in a small number of places, questions I address more fully in my article on manuscript transmission. Some are theological, where two true statements sit in tension that our finite minds cannot fully resolve, the interplay of divine grace and human responsibility being one example. And some difficulties are moral, where a command or an event, read at surface level, appears to jar with the character of God revealed everywhere else in Scripture.

Distinguishing these categories matters, because the tools for resolving them differ. A historical difficulty often yields to careful study of the ancient context, the kind of background a good study Bible or commentary can supply fairly quickly. A moral difficulty usually requires reading the troubling passage within the larger redemptive story, remembering that Scripture regularly describes sinful human behaviour without endorsing it, and that God’s dealings with a specific nation at a specific moment in redemptive history are not a timeless template for personal ethics. A theological difficulty, by contrast, often calls for patience rather than a tidy resolution, since Scripture itself sometimes holds two true things in tension without fully explaining how they cohere, trusting the reader to accept both on the authority of the text rather than resolving the mystery by denying one side or the other.

The Principle of Scripture Interpreting Scripture

My own consistent approach to any difficult Bible passage is to let clearer texts illuminate obscure ones rather than building a system on the hardest verse in the Bible while ignoring a hundred plainer ones. This principle, sometimes called the analogy of faith, treats Scripture as its own best interpreter. Where Genesis is unclear, the rest of the Pentateuch, the Prophets and the New Testament’s own use of Genesis usually shed real light. Where Revelation’s imagery is obscure, the Old Testament prophetic backdrop it constantly draws upon supplies the vocabulary needed to read it responsibly.

This is why I encourage believers to resist the temptation to build an entire doctrine around a single ambiguous verse, however striking it sounds when quoted alone. Sound doctrine rests on the weight of Scripture’s full testimony, not on isolated proof texts wrenched from difficult, disputed corners of the text.

What Difficult Passages Are Not

I want to be equally clear about what difficult Bible passages are not. They are not evidence that Scripture contradicts itself, since claimed contradictions almost always dissolve once we account for differing purposes, audiences, or complementary rather than competing perspectives among the biblical authors. Nor are they evidence that inerrancy is a naive or untenable doctrine. Inerrancy concerns what the biblical authors actually affirmed in their original context and intent, not a demand that every genre read like a modern legal document with no figurative language, rounded numbers or selective emphasis.

You can read more on how this relates to the broader doctrine of Scripture in my articles on biblical inerrancy and on whether there are contradictions in the Bible, both of which treat this territory in more depth than I can cover here.

A Pastoral Word for the Struggling Reader

If you have hit a difficult Bible passage that has genuinely shaken you, I want to say something directly to you. Do not panic, and do not assume your questions are unwelcome or evidence of unbelief. Bring the question honestly to the Lord in prayer, consult a trustworthy commentary, ask a mature believer you respect, and give yourself permission to hold a small number of things with an open, patient hand while your confidence in the whole rests on the overwhelming weight of what Scripture makes abundantly clear. The Bereans, commended in Acts 17:11 for examining the Scriptures daily, model exactly this posture of diligent, unafraid inquiry when facing a difficult Bible passage of their own. The NET Bible study notes on Joshua are a good example of the kind of careful background work that resolves many apparent moral difficulties in the conquest narratives.

I have found, across years of pastoral ministry, that almost every difficulty that once troubled me deeply has either resolved with further study or settled into a manageable, minor mystery that no longer threatens my confidence in the gospel itself. Very few, if any, remain genuinely unresolved after patient, prayerful investigation. The Greek word Peter uses for hard to understand things, δυσνόητος, dysnoetos, simply means difficult to grasp, not impossible, and that distinction matters a great deal.

A Concrete Example: The Genocide Texts of Joshua

It is worth working through one genuinely hard case of these difficult Bible passages rather than speaking only in generalities. The conquest narratives in Joshua, where God commands the Israelites to destroy the Canaanite nations, are among the most difficult Bible passages many readers ever encounter, and I will not pretend the tension disappears with a glib one-line answer. What helps me is remembering the specific, bounded, historical nature of this command: it was directed at particular nations under prolonged divine patience for centuries of entrenched wickedness, including child sacrifice, and it functioned as an act of righteous judgement carried out at a specific moment in redemptive history, not a timeless template for how believers should treat unbelieving neighbours today.

The New Testament nowhere repeats or extends this pattern for the church age. Instead it commands us to love our enemies, to bless those who persecute us, and to proclaim the gospel rather than wield the sword against unbelief, a stark contrast that itself shows the conquest narratives were tied to a unique redemptive-historical moment rather than a universal moral principle.

So, now what?

So, having worked through several categories of difficult Bible passages together, what do we do with them practically? We hold them honestly rather than pretending they do not exist, we study them with the tools God has given His church across two thousand years of careful scholarship, and we let the overwhelming clarity of Scripture’s central message, who Jesus is, what He accomplished, how we are saved, anchor us while the smaller, harder corners are worked through in their own time.

A book with no difficulty at all would be a book too shallow to hold the mind of God. I would rather wrestle with a handful of genuinely hard passages within a book that has proven itself utterly trustworthy everywhere else, than trade it for something simpler and shallower. Keep reading, keep asking, and keep trusting the God who gave you this book in the first place.

There are some things in them that are hard to understand, which the ignorant and unstable twist to their own destruction, as they do the other Scriptures.

2 Peter 3:16