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Troubleshooting Common Reconciliation Issues

The beginning balance in QBO does not match my bank statement.

The beginning balance of one reconciliation should always be the same as the ending balance of the prior reconciliation. If the prior reconciliation was done correctly and does, in fact, match the ending balance on the prior statement, then a change was made to a reconciled transaction. When this happens, there will be a box in the reconciliation screen that says, "Hold on! Your account isn't ready to reconcile yet." You can see the details of what was changed by clicking "We can help you fix it."

  • The amount of a reconciled transaction has been changed. Solution: Note the amount of the transaction at the time it was reconciled. Click "View" next to the transaction to open the transaction. Restore the original reconciled amount. Save and close the transaction.

  • The reconciled status was removed in the account register. Solution: Locate the check in the account register. Click the status column until the R appears. This will restore the reconciled status.

  • A reconciled transaction was deleted. Solution: Click "View" next to the transaction to see the details. Re-enter the transaction.

  • The Bank Account on a reconciled transaction has been changed. Solution: Locate the transaction in the account register. Open it and change the bank account. Save and close. View the account register and restore the reconciled status.

Now, reconcile the account using the same date and ending balance of the last reconciliation. Check off the missing transaction(s). When the Difference reaches zero, click "Finish now."


I have old, uncleared transactions that need to be deleted.

  • For Deposits, enter an expense in the current period that uses the same category as the original deposit.

  • For Checks, enter a deposit in the current period that uses the same category as the original check.

  • For Bill Payments, enter a deposit in the current period that uses the same category as the original Bill.

Reconcile the account using the same date and ending balance of your last reconciliation. Clear both the original transaction and the new transaction. When the Difference is zero, click "FInish now" and "Done."


After checking all transactions that have cleared the bank, I still have an amount in Difference.

There are four numbers involved in any reconciliation:

  1. Beginning Balance

  2. Deposits and Other Credits

  3. Checks and Payments

  4. Ending Balance

So ask yourself these questions and you will find where the discrepancy lies:

  1. Does the Beginning Balance match the bank statement?

  2. Do the total Deposits and Other Credits match the bank statement?

  3. Do the total Checks and Payments match the bank statement?

  4. Does the Ending Balance match the bank statement?

There are payments in the Payments to Deposit window that have already been deposited and need to be cleared.

This will happen when a customer payment is correctly posted using Receive Payment, but is incorrectly added to the Bank Deposit by entering the information in the "Add funds to this deposit" section of the Bank Deposit. If this issue is not resolved, the result is overstated income and overstated Undeposited Funds.


There are two ways this can be resolved:


OPTION 1: Correct each deposit individually:

  1. Find and open the deposit.

  2. Check the box next to the payment being deposit.

  3. Delete the line with that payment in the "Add funds to this deposit" section.

  4. Click "Save and close" after verifying that the amount of the deposit has not changed.

OPTION 2: Clear all customer payments with one deposit:

  1. Start a new Bank Deposit.

  2. Select all payments that need to be cleared.

  3. In the "Add funds to this deposit" section, enter the same income account in the "Account" column as the invoices the customer payments are clearing.

  4. Enter a negative amount in the "Amount" column to zero the deposit.

  5. Click "Save and close."

If you have any questions or need assistance troubleshooting any issues, please let us know!

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