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gjhbhines
February 3, 2026
Solved

How do I fix a reconciliation discrepancy caused by deleting transactions that were part of a previous reconciliation?

  • February 3, 2026
  • 2 replies
  • 192 views

Hi there - I have deleted some duplicate bills and bill payments that had not been caught and have been included in a previous reconciliation. Now that I'm trying to reconcile again to keep my books organized, I've received a flag for a discrepancy of the beginning balance. I'm struggling to find the right steps to fix. 
Thanks in advance!

Best answer by sofiamdc-2341

Deleting transactions that were already included in a past reconciliation breaks the beginning balance of your next reconciliation, because the closed reconciliation still "expects" those entries. The cleanest fix is to undo the affected reconciliation and re-reconcile, though that requires an accountant user. If you don't have one, you can address the discrepancy through the discrepancy report or by adjusting the reconcile status manually. Here's each path.

Path 1 (accountant user required): Undo and re-reconcile

  1. Open the client's company file from QuickBooks Online Accountant.
  2. Go to All apps, then Accounting, then Reconcile.
  3. Select History by account.
  4. Choose the account and date range, then find the reconciliation you want to undo.
  5. In the Action column, select the dropdown, then Undo, then Yes, then Undo again to confirm.

Important: undoing one reconciliation undoes that one and all reconciliations after it. You'll need to re-reconcile each affected period in order from oldest to newest.

After undoing, reconcile the account again. Check the transaction audit history for any transactions in the undone period that may have been changed manually.

Path 2 (any user): Review and resolve the discrepancy report

  1. Run the Reconciliation Discrepancy Report. The Total Discrepancy Difference on the report should show $0.00. If it doesn't, the entries shown are what's causing the difference.
  2. Check that the beginning balance in QuickBooks matches the beginning balance on your bank statement for the same period.
  3. Address each discrepancy item — in this case, the deleted transactions are the source — by either restoring the deleted transactions or adding a journal entry for the difference, then reconcile again.

Path 3 (any user): Manually remove transactions from a reconciliation

Use this if you want to un-reconcile specific transactions without undoing a full period.

  1. Go to Accounting, then Chart of Accounts.
  2. Find the account, then select View register.
  3. Select the transaction to expand it. In the Reconcile Status column (the checkmark column), you'll see an R.
  4. Select the box with the R and click through until the box is blank. This removes the transaction from the reconciliation.
  5. Select Save, then close the account register.

After removing a transaction this way, re-run the discrepancy report to confirm the difference clears before starting your next reconciliation.

Helpful Resources:

2 replies

Tori B
Tori BQuickBooks Team
QuickBooks Team
February 3, 2026

Hi there, @gjhbhines.

 

How's your day going so far? I hope all is well. 

 

In the past, we have seen users in this same position have their accountant's undo the last reconciliation. Then reconcile the transactions again so everything balances. 

 

Here's how you can undo the last reconciliation (please note your accountant is the only user that can preform these steps😞 

 

  1. Open your client’s company file in QuickBooks Online. Go to All apps, then Accounting, then Reconcile.
  2. Select History by account.
  3. Choose the account you want to unreconcile and the date range.
  4. Find the reconciliation you want to undo.
  5. From the Action column, select the dropdown, then click on Undo.
  6. Hit Yes.
  7. Select Undo.

 

Note: If you don't see Undo, make sure you've opened your client's company file from QuickBooks Online Accountant.

Result


The chosen reconciliation, and any reconciliations since then, are undone.

 

Transactions that remain in the register for the dates that were undone may have changed manually. Check your transaction audit history.

 

What’s next: After undoing the reconciliation, you can reconcile the account again and fix any errors.

 

If you don't have an accountant user you'll want to review everything on the discrepancy report. The Total Discrepancy Difference on the report should be $0.00. Then, check the beginning balance in QuickBooks. It should match the beginning balance on your bank statement.

 

Also, if you need to undo a past reconciliation, you have an option to do it manually.

 

Here's how: 

 

  1. Go to Accounting > Chart of accounts.
  2. Find the account that has the reconciled transaction. Then click the View register link.
  3. Select the transaction to expand the view, and in the Reconcile Status column (indicated by a checkmark ✔ column.) you’ll see an “R”.
  4. In the checkmark ✔ column, select the box with the “R” until the box is blank. This removes the transaction from the reconciliation.
  5. Hit Save.
  6. Close the account register.

To help manage your past and present reconciliations, please feel free to read these articles:

 

 

That should do the trick. Please don't hesitate to let me know if you have any additional questions or concerns. Have a great day ahead! 

sofiamdc-2341
sofiamdc-2341Community ManagerAnswer
Community Manager
August 18, 2026

Deleting transactions that were already included in a past reconciliation breaks the beginning balance of your next reconciliation, because the closed reconciliation still "expects" those entries. The cleanest fix is to undo the affected reconciliation and re-reconcile, though that requires an accountant user. If you don't have one, you can address the discrepancy through the discrepancy report or by adjusting the reconcile status manually. Here's each path.

Path 1 (accountant user required): Undo and re-reconcile

  1. Open the client's company file from QuickBooks Online Accountant.
  2. Go to All apps, then Accounting, then Reconcile.
  3. Select History by account.
  4. Choose the account and date range, then find the reconciliation you want to undo.
  5. In the Action column, select the dropdown, then Undo, then Yes, then Undo again to confirm.

Important: undoing one reconciliation undoes that one and all reconciliations after it. You'll need to re-reconcile each affected period in order from oldest to newest.

After undoing, reconcile the account again. Check the transaction audit history for any transactions in the undone period that may have been changed manually.

Path 2 (any user): Review and resolve the discrepancy report

  1. Run the Reconciliation Discrepancy Report. The Total Discrepancy Difference on the report should show $0.00. If it doesn't, the entries shown are what's causing the difference.
  2. Check that the beginning balance in QuickBooks matches the beginning balance on your bank statement for the same period.
  3. Address each discrepancy item — in this case, the deleted transactions are the source — by either restoring the deleted transactions or adding a journal entry for the difference, then reconcile again.

Path 3 (any user): Manually remove transactions from a reconciliation

Use this if you want to un-reconcile specific transactions without undoing a full period.

  1. Go to Accounting, then Chart of Accounts.
  2. Find the account, then select View register.
  3. Select the transaction to expand it. In the Reconcile Status column (the checkmark column), you'll see an R.
  4. Select the box with the R and click through until the box is blank. This removes the transaction from the reconciliation.
  5. Select Save, then close the account register.

After removing a transaction this way, re-run the discrepancy report to confirm the difference clears before starting your next reconciliation.

Helpful Resources:

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