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Pay your non-tax liabilities in QuickBooks Desktop Payroll

SOLVEDby QuickBooksQuickBooks Desktop Payroll15Updated April 15, 2022

Learn how to pay third-party agencies for your benefits or deductions in QuickBooks Desktop Payroll.

In QuickBooks Desktop Payroll, you can set up scheduled payments and create checks to pay benefits and other deductions to your plan administrators, such as 401(k), insurance premiums, or garnishments. This helps you stay on top of your bills and payments.

Need to pay taxes or file federal forms?  Use these links for more info.

We recommend setting up a payroll schedule for your non-tax liabilities to help you keep track of when they’re due.

Step 1: Set up your scheduled payment 

  1. Go to the Employees menu, then select Payroll Center.
  2. Select the Pay Liabilities tab.
  3. Under Other Activities, select Change or Manage Payment Methods.
  4. Select Benefit & Other Payments, then select Schedule Payments.
  5. Under the Benefits and Other payments column, select the benefit or liability you want to set up a schedule for. Then select Edit.
  6.  Select the Payee (Vendor).  
  7. Enter the Account Number. Then select the Payment Frequency.
  8. Select Finish to close the window.

Check out this video on how to set up your tax payment schedule.

Step 2: Add your scheduled payments to your calendar

  1. Go to the Payroll Center, then select Pay Liabilities.
  2. Place a checkmark next to the liability payment(s) for which a calendar reminder is needed.
  3. Select Set payment reminder dropdown menu.
  4. Select either “Add Reminder to Calendar” or “Export Reminder in Calendar File”
    • Add Reminder to Calendar will open the default calendar program on the user’s computer.
    • Export Reminder in Calendar File will create a calendar reminder file that can either be opened on the user’s computer, or that can be sent to other users to be added to their calendar program.

Note:  Basic and Enhanced Payroll users will be able to set payment reminders for payroll tax payments as well as other payroll liabilities like garnishments or benefits payments.  

Assisted Payroll users will only have the option to set payment reminders for other payroll liabilities since Intuit already pays the Federal and State taxes for Assisted Payroll customers.

  1. Go to Employees, select Payroll Taxes & Liabilities, then select Pay Scheduled Liability.
  2. In the Pay Taxes & Other Liabilities window, select the tax or other liability you want to pay from the list. Then select View/Pay.
  3. Review the dates and the amounts due. 
  4. Select Check/E-pay to proceed in paying your taxes.

Check out this video on how to pay your payroll taxes and liabilities.

  1. Go to Employees, select Payroll Center, then select Pay Liabilities.
  2. Under Other Activities, select Create Custom Payments.
  3. In the Select Date Range for Liabilities window, select a date range, then OK.
  4. Select To be printed if you want to print the liability check. Leave this clear if you issued a handwritten check.
  5. Select the bank account and the date you want to appear on the liability check.
  6. Choose either Review your liability check to enter expenses/penalties or Create a liability check without reviewing.
  7. Select the payroll item you want to pay, then select Create
    Note: For multiple payroll items, if the items are paid into one agency they are combined into one liability check. Different agencies will produce multiple liability checks. Make sure the check amount and item list under Payroll Liabilities are accurate.
  8. If you select Review your liability check to enter expenses/penalties, a liability check appears. If you didn’t, you can view the liability check in the check register.
  9. Make sure the date and amounts are correct. Select Print to print the check. 
  10. For a handwritten check, clear the Print Later checkbox. Then enter the check number or other reference in the NO. field. 
  11. For liabilities paid by Electronic Funds Transfer (EFT), clear the Print Later checkbox and type EFT in the NO. field of the liability check.
  12. Go to the Expenses tab if you want to enter expenses/penalties on the liability check.
  13. From the Account field drop-down, select the expense account you use to track payroll expenses and penalties, then enter the amount in the Amount column.
  14. Select Recalculate.

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