How to Fix Reconciliation Discrepancies in QuickBooks Online

A reconciliation discrepancy means an account that used to match the bank no longer does, and the usual reason is that something already reconciled was changed later. Find what changed, put it back, and only then reconcile the next period. Forcing the difference to zero with an adjusting entry hides the error instead of fixing it.

What a reconciliation discrepancy is

When you reconcile, you match QuickBooks to the bank statement line by line. Intuit's instruction is short: "Continue matching until the Difference is $0.00" (Reconcile an account in QuickBooks Online). A discrepancy shows up later, when the beginning balance of the next reconciliation no longer equals the ending balance of the last one, or when the difference refuses to reach zero.

QuickBooks has a default account for this situation. Intuit describes the Reconciliation Discrepancies account this way: "This account is created if you reconcile an account and the transactions in QuickBooks Online don't match the transactions reported on your bank statement" (Manage default and special accounts). If a file you inherit has a balance there, someone already pushed a reconciliation through without fixing it.

The four causes Intuit lists

Intuit's article on beginning balance issues (Fix beginning balance issues when reconciling in QuickBooks Online) names what usually breaks a past reconciliation:

"An incorrect opening balance entered when the account was created in QuickBooks."
"A reconciled transaction was edited, deleted, voided, moved, or unreconciled."
A categorized bank-feed transaction that was undone and sent back to pending.
"A transaction dated before your last reconciliation's ending date that was reconciled manually."

On a file you inherited, check the second cause first. Someone deletes what looks like a duplicate, or edits an old amount to make a report look right, and every reconciliation after that date stops tying out. The same article also sets the permission: "You need admin access to view and edit reconciliations."

How to fix it, step by step

Find the first period that stopped matching. Work from the oldest month forward. Fixing a later month first only moves the gap.
Find what changed after that period was reconciled. The audit log is the fastest way to see edits and deletions. Intuit notes that "Events recorded in the audit log are available for two years" and that "you can't turn off the audit log" (Use the audit log in QuickBooks Online).
Put the transaction back the way it was reconciled. Re-enter a deleted transaction, or restore the original date or amount, then check that the beginning balance matches the last statement again.
Reconcile the current period. Only after the history ties out, match the new statement until the difference is $0.00.

When to undo a reconciliation instead

Sometimes the cleanest path is to undo a reconciliation and redo it. Know two things first. Who can do it: in QuickBooks Online Accountant, "You can undo a reconciliation if you're the primary admin, an accountant user, or an in-house accountant." What it costs: "Undoing a reconciliation also undoes every reconciliation after it" (Undo a client's entire reconciliation in QuickBooks Online Accountant). Intuit's QuickBooks Online article adds: "Undoing a reconciliation is irreversible. It also permanently deletes associated reports and attachments" (Undo or remove transactions from reconciliations). Save any reconciliation reports you still need before you undo anything.

Why an adjusting entry is a last resort

QuickBooks lets you post an adjusting entry so the difference reads zero. Intuit calls it "a last resort" and warns that "making them for large discrepancies can cause accounting issues" (Enter an adjusting entry for a reconciliation). A plug makes the number look right while the transaction that caused the gap stays wrong, and the next person who reconciles inherits the problem.

Where duplicates come in

Many discrepancies start with a duplicate that someone deleted after the period was already reconciled. If you are about to remove duplicates from a file that has been reconciled, read how to find and delete duplicate transactions in QuickBooks Online first.

Before you reconcile a messy file, it helps to know what else is in it. CleanupLedger's free diagnostic reads a QuickBooks export and flags likely duplicates, uncategorized transactions and Opening Balance Equity activity, so you see the scope before you start.

FAQ

Why won't my reconciliation difference go to zero in QuickBooks Online?

Something in the period doesn't match the statement: a missing or duplicated transaction, a wrong amount, or a beginning balance that moved because an earlier reconciled transaction was edited or deleted. Fix that transaction, then keep matching until the difference is $0.00.

What causes a reconciliation discrepancy in QuickBooks Online?

Intuit lists four causes: an incorrect opening balance, a reconciled transaction that was later edited, deleted, voided, moved or unreconciled, a categorized bank-feed transaction that was undone, and an older transaction that was reconciled manually.

Who can undo a reconciliation in QuickBooks Online?

In QuickBooks Online Accountant, Intuit says the primary admin, an accountant user or an in-house accountant can undo a reconciliation. Undoing one also undoes every reconciliation after it.

Should I use an adjusting entry to fix a reconciliation discrepancy?

Only as a last resort, for a small difference you understand. Intuit warns that adjusting entries for large discrepancies can cause accounting issues.

Sources

Official Intuit QuickBooks documentation, checked September 24, 2026. Quotes are copied from these pages.