QuickBooks bank reconciliation discrepancy

When a QuickBooks Online reconciliation will not reach a difference of 0.00, the cause is nearly always one of four things: a missing transaction, a wrong amount, a duplicate entry or a wrong opening balance. QuickBooks has its own tools for each.

1. Use the Reconciliation Discrepancy Report

If the beginning balance on the reconcile screen is not what you expect, QuickBooks shows a link to fix it that opens the Reconciliation Discrepancy Report. It lists transactions that were changed or deleted after they were reconciled. Open each item, read what happened and the transaction history, then correct the entry so it matches your records or the statement. Fixed items drop off the report. You are done when the total discrepancy difference is 0.00.

2. Look for reconciled items you did not expect

Open the bank account's register and filter by reconcile status. A transaction marked R (reconciled) that is dated after your last completed reconciliation is a common cause. Change it back to uncleared; Intuit has an article on undoing or removing transactions from a reconciliation.

3. Check the statement values you typed

Re-check the ending balance and ending date. On a credit card or other liability account the sign of the ending balance matters: enter what you owe as a negative number if that is how the statement shows it.

4. Find who changed what

An admin can open Settings > Audit log, filter to all users and the reconciliation period, and see edits and deletions of the transactions involved.

5. Undo the reconciliation if needed

If past reconciliations were damaged, the cleanest fix is often to undo the affected reconciliation and do it again. Who can undo depends on your user role, so check yours before you plan around it.

6. An adjustment is the last resort

QuickBooks can add a reconciliation adjustment to force the difference to 0.00. Use it only for a small amount you have tried and failed to trace. It hides the cause instead of fixing it. If you find the real cause later, remove the adjustment and fix the transaction.

Sources

Checked against the vendor's own help pages on 6 November 2026. Menu names and report layouts change between plans, regions and releases, so confirm them on your screen.

• Intuit: Fix beginning balance issues when reconciling in QuickBooks Online
• Intuit: Why do deleted or changed transactions still appear on the Reconciliation Discrepancy Report?
• Intuit: Why is my beginning balance wrong when I reconcile in QuickBooks Online?
• Intuit: How to complete a bank reconciliation in QuickBooks Online