What to Do When Your Reconciliation Balance Doesn’t Match Your Bank Statement

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You’re in the home stretch of reconciling your bank account in QuickBooks, only to be met with that frustrating message: “Your reconciliation doesn’t balance.” We’ve all been there and while it can be discouraging, it’s totally fixable.

The key is knowing where to look for discrepancies and how to correct them without compromising your records. Whether you're off by a few cents or a few hundred dollars, this guide will walk you through what to do when your reconciliation balance doesn’t match your bank statement.

First, Ask Yourself These Questions

Before diving into the transaction list, take a moment to rule out some of the most common user errors:

Is this the first time I’ve tried to reconcile this account?

If so, double-check the beginning balance you entered. It should match exactly with the ending balance on the previous month’s bank statement - or, if this is your first reconciliation, the balance on the date you started using QuickBooks.

Did I skip entering a beginning balance - or enter the wrong amount?

A missing or incorrect beginning balance will throw off your reconciliation from the start. Go back and confirm that you’ve entered the right amount based on your statement. This often happens when people set up an account but forget to enter the initial balance.

Have I voided, deleted, or edited any previously cleared transactions?

If you’ve made changes to transactions that were already reconciled (like adjusting an amount, deleting a charge, or voiding a deposit) it can cause your reconciled totals to no longer match your actual bank activity.

Did I accidentally change the cleared status of a transaction?

Sometimes, while working directly in the check register, it’s easy to accidentally mark a cleared transaction as uncleared (or vice versa). Even a single checkbox can throw your reconciliation off balance.

Are all of the transactions from the bank statement checked?

Occasionally, you’ll have too many transactions (or not enough) marked as cleared on the reconciliation page. Some may appear to fall within your statement’s date range but actually cleared the bank on a different day. These small mismatches can throw your reconciliation off just enough to leave you scratching your head.

How to Correct the Discrepancies

Once you’ve identified the potential cause, here’s how to fix it:

1. Re-enter Missing or Deleted Transactions

If a reconciled transaction was deleted or never entered, re-create it using the original date and amount from your bank statement. Then manually mark it as cleared in the reconciliation window.

2. Edit Existing Cleared Transactions

If the amount of a previously cleared transaction has been changed, edit it back to match the original amount shown on the bank statement at the time of the original reconciliation. This helps restore consistency and resolve any imbalance.

3. Undo Previous Reconciliations 

If you’re unable to identify the issue or if multiple months are off, it may be best to undo your previous reconciliations. Work backward until you find a reconciliation that balanced properly, then redo each month, one at a time, ensuring each statement matches exactly before moving forward.

Note: In QuickBooks Online, this may require the help of your accountant or bookkeeper with Accountant access.

4. Review All Checked Transactions 

Pull up your bank statement and compare it to all checked items on the reconciliation page. Start by looking at the last few transactions to see if they show up on your bank statement. Uncheck any that aren’t on the statement.

If all else fails, uncheck all transactions on the reconciliation page and re-check them one by one as you go through your statement. This simple reset often catches entries that QuickBooks Online tried to pull into the reconciliation, even though they don’t actually appear on your bank statement for that period.

Pro Tips to Avoid This in the Future

• Lock your reconciled periods once completed to prevent accidental changes.

• Avoid editing, voiding, or deleting reconciled transactions unless absolutely necessary.

• Make it a habit to reconcile every month right after your bank statement becomes available.

• Always compare your beginning balance to the prior month's ending balance before starting a new reconciliation.

  
  

Final Thoughts

A reconciliation mismatch isn’t the end of the world - it’s just a signal that something needs attention. With a little detective work and some patience, you can identify the issue and bring your books back into balance.

And remember: regular, accurate reconciliation is one of the most powerful tools you have for protecting your business’s financial health.

Need help keeping everything on track? Grab our free DIY Bookkeeping Health Checklist – it walks you through the key habits to maintain clean books and avoid surprises like reconciliation errors.