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Level 3

Payroll Liabilities Double Payment

While attempting to reconcile our bank statement, I found that our State withholding taxes were withdrawn twice for a particular pay period.  I am also trying to run my quarterly withholding tax return. 


So the tax return of course shows balanced but really we have an overpayment and should receive a refund.  I tried creating a custom liability payment (didn't work), tried writing a normal check from the liability account (didn't work).


Can someone please advise how to enter this double payment into Quickbooks so that it will show up on the tax return as an overpayment?


Thank you!

6 Comments 6
QuickBooks Team

Payroll Liabilities Double Payment

Hey there, CCNCem. 


Thanks for dropping by this afternoon. What you're going to want to do is delete the tax overpayment. Doing this will allow you to enter the correct payment. To do so, follow along below:

  1. Click Taxes in the left panel.
  2. Go to Payroll Tax.
  3. Click View Tax Payments you have made and delete it. 

I would also recommend reaching out to an accountant, just to be sure your books are in order and, as always, you can contact our customer care agents if you'd like someone to be with you as you go through these steps. They can pull up your account in a secure environment and assist you further.


To reach us, please follow these steps:

  1. Sign in to your QuickBooks Online company.
  2. Click (?) Help at the upper right corner.
  3. At the bottom, click on Contact us.
  4. Type in your concern then hit Continue.
Level 3

Payroll Liabilities Double Payment

I don't have an overpayment in Quickbooks.  I have a payment withdrawn from my bank account twice.  It was not entered in Quickbooks twice.  I'm trying to find out how to enter the overpayment in QB so that it shows on my tax return as overpaid and I can get a refund from the tax agency.

QuickBooks Team

Payroll Liabilities Double Payment

Hello there, @CCNCem.


Since you've made mention that it's not an overpayment and it just needs to be recorded to show tax return as over paid and get refunded from the tax agency, therefore, applying it as payroll liability overpayment as a credit is not the best option.


With that being said, I recommend contacting our QuickBooks Desktop Payroll support team to have a check on your account and guide you through the process on how to record your tax overpayment.


You can reach our support using this link:


 Here are some related articles about managing your QuickBooks Desktop Payroll: 

It's my pleasure to assist you further if you have an additional concerns. Have a good day


Level 1

Payroll Liabilities Double Payment

I know this question was over a year ago, but I just had the same problem and figured out how to manually enter the extra payment in Quickbooks. Under the "Employees" tab, scroll down to "Payroll Taxes and Liabilities" and then "Create Custom Liability Payments". Once there you will set the dates for the payroll, the date of the payment, and then click on the various liabilities you want to pay. Enter the amount for each and then hit "Create". (separate ones for EDD and US Treasury payments)


I'm about to prepare the Quarterly return that includes the overpayment so hopefully it shows up and the refund process is straightforward. Hope this response helps anyone else who has accidentally double paid!

Level 1

Payroll Liabilities Double Payment

Thank you searnest this was very helpful!

Level 1

Payroll Liabilities Double Payment

Thank you searnest! Appreciate you took the time to respond because it definitely saved me a lot of time and helped me record this type of transaction.

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