How to Set Up E-File & E-Pay in QuickBooks Desktop & Online Payroll to Pay Taxes

We are delighted to see our users here in the QuickBooks Community. We are here to assist users on how […]

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We are delighted to see our users here in the QuickBooks Community. We are here to assist users on how to pull up the report which they might need in QuickBooks Desktop Pro version.

Here you will learn about how to set up e-file & e-pay in online payroll to pay taxes, so that you can electronically pay your state payroll taxes and file state forms.

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For making the payment for the state payroll taxes and filing the necessary state forms on time all over the year is an indispensable task. In QuickBooks Desktop Payroll upgrade, users can make the payment for taxes and file forms electronically for most states. This is the fastest and easiest way to ensure to stay compliant with the state agencies.

Set Up E-File & E-Pay in QuickBooks Desktop Payroll Enhanced

There’s a few set up tasks that you are required to complete prior to using e-file and e-pay in QuickBooks Desktop Payroll Enhanced.

Step 1: Grasp about State File and Pay Methods in QuickBooks

Every state tax has a specific way to make the payments & file forms in QuickBooks. Below are a few definitions given which are helpful to assist the user to understand the various ways.

  • E-file and E-pay together: The e-payment and e-filing are generated in the same step and sent to the state agency at the same time.
  • E-file & E-pay separately: There are two various steps which can be made and sent to the state agency at various times, and they are e-payment and e-filing.
  • E-file only: Users can e-file the form, but cannot use e-pay for tax payments. User can create and print the tax payment to forward to the state agency.
  • E-pay only: User can e-pay the tax payment, but cannot e-file the form. Users can prepare and print the tax form to forward to the state agency.
  • No e-file/e-pay: Users cannot pay taxes or file forms electronically in QuickBooks. User can create and print checks and state tax forms in QuickBooks to send to the state agencies.
  • Make file to upload: Various people who use the QuickBooks service can make a State Unemployment file in QuickBooks & manually upload it to the state agency.

Step 2: Register with Your State Agencies

If the user is not already registered with the State Withholding and State Unemployment Insurance tax agencies, he or she is required to do so user can pay your taxes and file the forms. The agencies will provide the user with an account number, the tax rates, deposit frequency, and if required, login credentials to their websites for payments and forms.

Step 3: Scheduled Payment Setup in QuickBooks

Scheduled payments in QuickBooks assist the user to retain the track of when the payroll taxes are due, so the user does not miss a payment. User can set up scheduled payments even if the user cannot use e-payments in QuickBooks.

  • Choose Employees, choose Payroll Taxes and Liabilities, and choose Edit Payment Due Dates/Methods.
  • Choose Schedule payments.
  • Choose the state tax user wish to schedule first, and choose Edit.
  • From Payment method, choose Check or E-pay.
  • Write the state account number.
  • Choose the Payment Frequency provided to the user from the state agency.
  • Repeat steps 3-6 for each state tax. When finished, choose Continue.
  • Choose the bank account you’ll use to track e-payments in QuickBooks, then choose Edit. This will help to match the bank account which user has used to register with the state agencies.
  • Enter or review the Account number and Routing number, then choose Finish.
  • For e-payments: review the info to make sure you’re correctly enrolled with the state agencies. User can take the print the info if required, post that shut the Enrollments window.
  • Once you are done, choose Finish.

Step 4: Set up E-file in QuickBooks

If the user is able to e-file your payroll tax forms in QuickBooks, you’ll need to set this up.

  • Choose Employees, and choose Payroll Center.
  • From the File Forms tab, under Other Activities, choose Manage Filing Methods.
  • Choose Continue.
  • Choose the state form you want to e-file, and then choose Edit.
  • Choose e-file, then choose Finish.
  • Repeat steps 4-5 for each state form.
  • When you’re done, choose Continue, then Finish.

QuickBooks Online Payroll

QuickBooks Online Payroll will naturally generate and process various payroll tax forms if the users have opted to have us file them for them, and have completed the e-file and e-pay enrollment.

If the users have opted out of automatic tax payments and form filing status, or if the users have not completed the e-file and e-pay enrollment, they are required to manage the tax payments and filings in the Payroll Tax Center. To assist the user to make the payment and file payroll taxes by themselves QuickBooks Online Payroll gives the users all the required instructions.

To get an automated tax payments and form filings, or to be allowed to begin with the payments and filings electronically using QuickBooks, complete any e-file and e-pay setup tasks on the To-Do List. To check the To-Do List:

  • Navigate to the Payroll and after that choose Overview.
  • Adhere the on-screen steps to finish the tasks or add missing info. This might involve the adding a bank account or the entering tax information.

QuickBooks Online Payroll Enhanced

  • From Setup, choose Update Electronic Services.
  • Choose Add / Edit Electronic Services.
  • Choose Start.
  • Choose Yes, I want to electronically pay and file my payroll taxes through my payroll account.
  • Enter bank account and principal officer info.
  • Review banking and principal info entered. Choose Back to modify or confirm to proceed.
  • Confirm IRS details for your business, then Continue.
  • Choose electronically if you want to enroll in state e-file and pay. If you need to enroll an additional state later on, go back to this page and choose your new state.
  • Choose your service fee payment method, and then Continue.
  • Choose Show my forms.
  • Print, sign, and contact our team to send or upload the authorization form. From the Help section in the online payroll, choose Contact us to connect with a payroll support.

Once authorization forms have been received and bank info has been confirmed, we’ll process the enrollment. Users will get an email as soon as the payroll account is active for E-File & Pay. Note that each state has a various enrollment lead time.

This article tells you about the several features of QuickBooks Payroll Reports in detail, from its use to the steps which user can adhere to set up a QuickBooks Payroll Report comfortably.

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I need to add an Additional State for Taxes. How does the user Enroll the Latest State for E-services?

Kindly adhere the below given steps to enroll new state for e-services:

Enter the new state info.
Go along the E-File & Pay enrollment again. Kindly adhere the steps given above for the product.
In some cases, you are required to send additional forms. Contact us to send the forms. From the Help section in your online payroll, choose Contact us to connect with a payroll support.
You’ll receive an email as soon as you can e-file and pay taxes for the new state. Kindly know that the enrollment lead time differ according to the state.

I don’t have an Unemployment Account Number as my Business is Exempt for Unemployment Taxes. How can I Proceed with the Enrollment?

Contact us to assist you with completing the enrollment process. From the Help section in your online payroll, choose Contact us to connect with a payroll support.

It has been Weeks since the Enrollment, but I still can’t E-file and Pay my Taxes. When can I make the Payment and File Taxes Electronically?

We can check the status of the electronic services enrollment for you. From the Help section in your online payroll, choose Contact us to connect with a payroll support.

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Why should do you change the Employee status instead of deleting them on QuickBooks?

If you are unable to see the option to terminate an employee on your list of active employees on the company payroll, this mostly implies that they have some history. Thus, if you change the employee status instead of deleting it on QuickBooks, the profile and pay records remain in your accounting database without any data loss in your tax payments.


Is it possible to use the Direct Connect option to sync bank transactions and other such details between Bank of America and QuickBooks?

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