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Level 2

Accidental double tax payment

We switched from Quickbooks Online to Quickbooks Enterprise Desktop in the middle of Q3 2023.  In QBO we had taxes set to autopay.  We learned too late that QBO still paid the Q3 taxes even though we had switched to QBDT Enterprise.  What this meant was that we paid a partial Q3 941 from QBO, and a full (correct) Q3 941 from QBDT.  The IRS refunded us both payments as the easiest solution for them, and then sent us a bill for the correct amount (now plus interest and fee).  My question do i record the refund check since my current QBDT doesn't have a record of the QBO Q3 941?  I assume I need to enter that somehow.  And then I need to get QBDT to pay the 941/940 bill (with interest and fees) that we have just received.

3 Comments 3
QuickBooks Team

Accidental double tax payment

Thank you for posting in the Community, Finaco.


I'm here to help you record the accidental double tax payment in QuickBooks Desktop (QBDT).


Yes, you need to enter the QuickBooks Online payment in QBDT. To do this, let's use the payroll setup window. Here are the steps you need to follow:


  1. Access the Payroll Setup Interview.
  2. Proceed to step 5 Year-to-Date Payrolls.
  3. Click Continue.
  4. If your company has issued paychecks this year, choose Yes and select Continue.
  5. On the next screen, select the option Tax Payments and then click on Edit.
  6. Print the Tax Payments Checklist and consult with your accountant before proceeding.
  7. Select the arrow next to the quarter you'd like to enter tax payments in.
  8. When a quarter is selected, the window will open all taxes owed within that quarter. There will be three columns: QuickBooks - Calculated Amount, Total Amount You've Already Paid, and Balance Remaining. Enter the payroll tax payments you've made.
  9. Once all payments have been entered for a quarter, select the next quarter and repeat the process until all tax payments have been entered.
    • If no tax payments have been made, Total Amount You've Already Paid should be empty and columns one and three should match. If they do not match there may be issues when the prior payroll was entered. Which will need to be addressed and corrected before continuing.
    • Once the payments are entered, balances in Balance Remaining may need to be paid.
  10. Hit Done Entering in Tax Payments when you have completed entering payments.


You can also record tax payments outside of the Payroll Setup window. Please refer to this article for the steps: Enter historical tax payments in Desktop payroll.


After entering the payments, let's take care of the tax refund from the Internal Revenue Service (IRS). Please note that if the refund is from a period before you used our payroll service, you’ll need to enter the refund check as a deposit to your bank account. If not, you can follow these steps:


First, you'll need to find a matching refund amount in QuickBooks by running a payroll liabilities balance report. If you don't find an amount that matches, review the refund notice. The check may include interest, or some of your refunds may have been applied to past-due taxes. Then, let's enter a payroll liability refund check. If the refund amount matches the report without interest or partial refund, here's how to create the appropriate refund check:


  1. Go to Employees, and select Payroll Taxes and Liabilities.
  2. Click Deposit Refund Liabilities.
  3. In the vendor dropdown, select the agency that sent the refund check.
  4. In the Refund Date field, enter the deposit date.
  5. In the For Period Beginning field, enter the first day of the pay period that the refund affects.
  6. Select how you want QuickBooks to handle the deposit:
    • Group with other undeposited funds: adds the amount to a holding account. This option requires you to use Make/Record Deposit to complete the process.
    • Deposit To: Record the amount to the account of your choice.
  7. In the Taxes and Liabilities section, select the payroll items affected by the refund.
  8. In the Amount column, enter the amount of the refund as a positive number.
  9. Hit OK.


Please note that if you use QuickBooks Desktop Payroll Assisted, you'll need to send the tax adjustments to us. If the refund check includes interest, you'll need to follow the steps in this article: Handle a payroll tax refund.


You might find it helpful to access your prior tax forms and payments. Check out this resource to learn more: View your previously filed tax forms and payments.


If you have any other concerns about managing tax payments in QuickBooks, please don't hesitate to leave a reply below. I'll be around to lend a helping hand.

Level 2

Accidental double tax payment

Thank you for your help.

One question, does the fact that the payment in question is in FY 2023 instead of 2024 mean that I should NOT do the Payroll setup interview?  (an early step there said to enter YTD taxes paid, and these were paid in 2023, not 2024).



Irene R
QuickBooks Team

Accidental double tax payment

Hello there, Finaco.


I appreciate you returning to the thread with further inquiries regarding the refund check recorded in your QuickBooks Desktop (QBDT) account.


I understand that my colleague has provided you with the correct information. However, based on the scenario you have presented, I would like to clarify that you do not need to go through a Payroll Set-up interview. Since the payment in question dates back to the Fiscal year of 2023 and falls under a different set of regulations. It does not require the same process as payments made in the current year. 


Furthermore, in recording your deposit refund liabilities, you can refer to the steps and details provided by my colleague previously mentioned. 


In addition, learn how to obtain your prior tax forms and payments by visiting this article: View your previously filed tax forms and payments.


I hope this clears up any confusion, but please let me know if you have any further questions or concerns about managing your tax payments in your QBDT. The Community will always be here to assist you.

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