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E-file and e-pay state tax forms together

Learn how to e-file and e-pay state tax forms together in QuickBooks Desktop.

Some State Tax Agencies require that you file your payment and forms together and that you use the same submission method. Therefore, if you e-pay your payment, you must e-file your form, too. We explain what you can and can't do. As well as how to set it up.

Requirements to e-file and e-pay State forms and taxes together in QuickBooks Desktop

For all other state taxes, E-file and E-pay separately.

State taxes that must be e-filed and e-payed together

The following taxes must be efiled and epayed together.

  • Connecticut Unemployment Insurance
  • Florida Unemployment Insurance
  • Indiana Withholding
  • Mississippi Withholding
  • Nebraska Unemployment Insurance
  • New York Unemployment Insurance
  • Ohio Unemployment Insurance
  • Utah Unemployment Insurance
  • Virginia Unemployment Insurance


States not supported for e-file and/or e-pay in QuickBooks Desktop

AlaskaHawaiiMinnesotaOklahomaSouth Dakota
ArkansasKentuckyNorth CarolinaPuerto RicoVermont
District of ColumbiaMassachusettsNew HampshireRhode IslandWest Virginia
DelawareMichiganNevadaSouth CarolinaWyoming

Things to remember

Things to remember as you file 

  • IN: To help QuickBooks Desktop Payroll subscribers who file the Indiana WH-1 and WH-3 tax forms, QuickBooks Desktop Payroll added a new user field labeled County subject to withholding to the employee setup for Indiana Counties Tax; and a new Excel report called Local Tax Summary. The new report will enable you to identify the amount of tax withheld for each county. (Find out more here.)
  • CT, FL, MS, NE, and UT: If you have made a payment or filing using something other than QuickBooks Desktop Enhanced Payroll you will not be able to E-pay and E-file together in QuickBooks Desktop. Your E-pay and E-file together submission will be rejected by the agency. You can print and mail your remaining filing and/or payment. You can also go to the agency website and make the payment or filing online.
  • For New York NYS1 form and payment: NY doesn't  allow a withdraw on date for the payment. The state will pull the payment when they receive the form submission.

You can check Payroll Tax Compliance for more details.

First time to e-file and e-pay

If this is your first time to e-file the state form and e-pay for the state tax liability, you need to enroll in your State Tax Agency.

Change the scheduled State tax payment method to E-pay

The State tax payment method and form filing method will be set to e-pay and e-file respectively. When you pay your State tax through e-pay, QuickBooks Desktop will e-file the appropriate state form with it.

  1. Go to Employees, then select Payroll Center.
  2. Select the Pay Liabilities tab. Under Other Activities select Change Payment Method. The QuickBooks Payroll Setup window will open.
  3. In the QuickBooks Payroll Setup window, select the scheduled payment you want to update and select Edit.
  4. In the Edit Payment Schedule window, select E-pay.
    A warning message will inform you that QuickBooks Desktop will automatically set up E-file for the State tax.
  5. Select OK.
  6. Select Finish. You will be back to the QuickBooks Payroll Setup window.
  7. Select Continue.
  8. Select the account you want to use for e-payments and select Edit.
    Note: This account will be used to track e-payments in QuickBooks Desktop only.  The actual bank account that will be debited for your payment depends on the account information you have submitted to your State Tax Agency upon enrollment.
  9. In the Edit Bank Account window, enter the Bank Account Number and Routing Numbeof the account you want to use for e-payments.
  10. Select Finish.
  11. Select Continue.
  12. Select Finish Later.

You can now e-file and e-pay together the State tax in QuickBooks Desktop.

E-file and e-pay together in QuickBooks Desktop

If you plan to make another E-payment for the same liability period for the same tax item, process the E-payment outside as QuickBooks Desktop Payroll does not allow more than one E-payment per liability period.
  1. Go to Employees, then select Payroll Center.
  2. In the Pay Scheduled Liabilities section, select the liability you are paying.
  3. Select the View/Pay button. The Tax Forms and Payments window will appear.
  4. Select Continue. The appropriate form of the state will open.
  5. Select Next to review all pages.
  6. To check for errors, select Check for Errors. You need to correct any errors detected to be able to proceed.
  7. After all errors are corrected, select Submit Form. The Submit Form dialog box appears.
  8. Select E-File & E-Pay.
  9. Select the Bank Account for the e-payment.
  10. Select the E-file & E-pay button.
  11. Enter the Contact phone number and E-mail address.
    Note: The information required on this screen will vary based on what is required by your State Tax Agency.
  12. Select Submit.
  13. The Submitted to Intuit window will appear.
  14. Select Print Confirmation. This will serve as a confirmation that Intuit has received your request.

Important: You need to check the status of your submission to the appropriate State Tax Agency. See Check e-payment or e-filing status.

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