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How to fix a reconciliation discrepancy in QuickBooks Online

A reconciliation discrepancy in QuickBooks Online shows up as a beginning balance that doesn't equal your last ending balance, and QuickBooks won't let you reconcile until the gap is explained. Start from the alert on the Reconcile page, which opens the Reconcile Discrepancy Report, then check the audit log and the account register for anything the report misses.

  • By Book Keeping Pros
  • Sources checked 17 Oct 2026
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Key takeaways

  • Each reconciliation should begin from the ending balance of the one before it, so a gap means a transaction has changed since then.
  • Deleted or voided transactions, and transactions marked R outside a reconciliation, don't appear on the Reconcile Discrepancy Report and have to be found in the audit log or the register.
  • On an account being reconciled for the first time, the usual culprit is the opening balance, which should equal the bank's balance on the same day.

Before you start

Gather the bank statements for the account and the period you're reconciling. Viewing and editing reconciliations needs admin access, so check your user has it.

Clear the bank feed for the period. Go to All apps, then Accounting, then Bank transactions, and make sure each transaction from that time is matched, categorised, posted or excluded. For an account connected to online banking, every downloaded transaction should be matched or categorised.

Write down exactly how far out the beginning balance is. The changes you uncover should add up to that difference, which is how you know when you've found them all.

Knowing the usual causes helps you spot them. Intuit names four: an opening balance entered wrongly when the account was set up; a reconciled transaction that was later edited, deleted, voided, moved or unreconciled; a categorised bank feed transaction that was undone and sent back to pending; and a transaction dated before the last reconciliation's ending date that was marked reconciled by hand. If this is the account's first reconciliation, go to the opening balance checks in the last section first.

Steps

  1. Go to All apps, then Accounting, then Reconcile.
  2. Pick the account from the Which account do you want to reconcile? dropdown. With several accounts at one bank, or more than one account of the same type, take care to choose the right one.
  3. Find the alert saying the account isn't ready to reconcile because the beginning balance is off, and select We can help you fix it. The Reconcile Discrepancy Report opens.
  4. Take the listed transactions one at a time. The What happened column shows what changed, when it changed and who changed it.
  5. Select Review in tray for the details. For a transaction's complete history, open the dropdown beside Review in tray and choose View history.
  6. Correct each change that was made in error, either with the fix the tray suggests or with your own correction from your records.
  7. If the report is clear and the balance is still out, go to Settings, then Audit log. Filter to the account and the period since your last completed reconciliation, and look for deleted or voided transactions.
  8. Next, go to All apps, then Accounting, then Chart of accounts, and select View register for the account. Filter by Reconcile status and look for anything marked R that's dated after your last completed reconciliation.
  9. Check that the Total discrepancy difference has come down to zero and that your corrections add up to the amount you wrote down.

Note

The tray's suggested fix assumes the change was a mistake, but some changes are deliberate. Leave those as they are. If a correction would alter a reconciled period or the opening balance and you're not certain about it, check with your accountant first.

What changes afterwards

Once every change is accounted for, the beginning balance agrees with your bank statement and QuickBooks lets you carry on with the reconciliation.

Some fixes ask you to reconcile a single transaction. There are two ways to do it: mark it R in the account register, or reconcile the account again using the same ending date and ending balance as your last reconciliation. Either corrects the beginning balance, but only reconciling again leaves the change recorded on a reconciliation report.

If the register search turns up a transaction that shouldn't be marked R, it can be set back to uncleared from the account history. The page on undoing a reconciliation has those steps.

If it doesn't work

On a first reconciliation, check the opening balance before anything else. From Accounting, open Chart of accounts, find the account and select Account history. The entry with Opening Balance in the Memo column carries the date and amount QuickBooks started from. Compare it with the balance on your bank statement, or in your online banking, for that same day. If they differ, select the entry, change the amount in the Deposit column to match the bank and select Save.

While you're in the account history, look down the tick column. On a first reconciliation the opening balance should be the only entry with an R, and everything else should show C or a blank box. Select any other R until its box is blank, then save.

An opening balance can leave out transactions that were still pending at the bank when the account was created. Intuit suggests setting it at the start of a bank statement, which makes the first reconciliation simpler. If no opening balance was ever entered, one can be added by hand later, and Intuit has separate steps for older transactions dated before it. If the balance still won't agree after all this, your accountant can help.

General information

This how-to follows Intuit's own help for QuickBooks Online. Screens change between versions, so if yours looks different, use the Intuit article in the sources. It is general information about using the software, not advice about your business. Sources checked 17 October 2026.

Sources

  1. Fix issues for accounts you've reconciled in the past, QuickBooks Online help (Australia)

    Intuit Australia Pty Ltd. Current at 17 October 2026, released 17 October 2026. Checked 17 October 2026.

    QuickBooks is a trademark of Intuit Inc. Licence: Intuit Australia legal terms (facts quoted with attribution, no endorsement implied).

  2. Fix issues the first time you reconcile an account, QuickBooks Online help (Australia)

    Intuit Australia Pty Ltd. Current at 17 October 2026, released 17 October 2026. Checked 17 October 2026.

    QuickBooks is a trademark of Intuit Inc. Licence: Intuit Australia legal terms (facts quoted with attribution, no endorsement implied).

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