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Pay and file payroll taxes and forms manually in QuickBooks

Pay and file payroll taxes and forms manually in QuickBooks

Income taxes, as well as taxes for Social Security, Medicare, and unemployment compensation, are all included in payroll taxes. It’s important to remember that taxes might be paid by either the employee or the firm. 

Learn how to use QuickBooks Desktop Payroll

Calculate and print payroll tax payments and documents so you can manually file them with the IRS and state agencies.

You can still prepare your Federal 941/944, 940, or state tax payments and forms in QuickBooks Desktop Payroll Basic, Standard, or Enhanced to submit to the tax agency if you can’t e-pay or e-file.

In some places, you can use QuickBooks Desktop Payroll to create a State Unemployment Insurance (SUI) file that you can then upload to the state agency’s website.

We pay and file your federal and state taxes for you if you use QuickBooks Desktop Payroll Assisted.

Let’s begin making your tax payments and forms

Create and print your payroll tax payment

Step 1: Set up a scheduled payment

To make sure that you don’t forget to pay your payroll taxes on time, QuickBooks’ scheduled payments feature can help. If QuickBooks does not support e-payments, you can still set up scheduled payments.

  • You have to select Employees, then you have to select Payroll Taxes and Liabilities, and finally Edit Payment Due Dates/Methods. 
  • Then you have to select Schedule payments.
  • Click Edit after selecting the state tax you wish to schedule first. 
  • Click Payment method and choose Check. 
  • Now enter your state account number.
  • Choose the payment frequency that the state agency sent to you. 
  • For every state tax, repeat steps 3-6. When you are done, you have to click Proceed.
  • After choosing the bank account for tracking payments in QuickBooks, you have to click Edit. The bank account you used to register with the IRS and state agencies should match this. 
  • Choose Finish when you are finished. 

Step 2: Create and print your tax payment

You can enter payments made to the federal government in QuickBooks. Through the IRS website, you will electronically send the payment. 

You can create and print the check to send to the state agency for the payment of state taxes. 

  • Begin by selecting Employees, then you have to click on Payroll Taxes and Liabilities, and then you have to select Pay Scheduled Liabilities. 
  • After choosing the desired tax from the list, click View/Pay. Review the taxes and amounts due.
  • Then you have to select Save and Close and then you have to select Print Checks.

Prepare and print your payroll tax forms

Step 1: Pay or record all tax payments

Pay all applicable taxes in QuickBooks before preparing your tax form. If you don’t, the form will show the amounts that are due. 

Step 2: Prepare and print or save your payroll tax form

  • Choose Employees, followed by W-2s and Payroll Tax Forms, and finally click Process Payroll Forms.
  • From the list, you have to choose the federal or state form that you want to create.
  • Then you have to select Create form.
  • After choosing the Filing Period from the drop-down menu, you have to click OK.
  • Fill out the interview section on your form. Complete the fields indicated in green and check any fields on the form that have already been filled in.
  • After choosing Next, you have to review each page of the form. 
  • Once complete, choose Check for Errors. QuickBooks will highlight any errors in the document.  These must be corrected before printing and saving the form.
  • Choose Save as PDF or Print for your Records if you are prepared to print and save your form.  Then, select Save and Close if you need to return to the form later.

Step 3: Send the form to the tax agency

Check the instructions page to find out where to mail your tax form after you have printed yours. 

Create an SUI file

Instead of filing a quarterly tax return, you can generate an SUI file in QuickBooks and submit it to the following state agencies: 

South Carolina, Vermont, Ohio, Pennsylvania, New Hampshire, Colorado, Indiana, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, and Nebraska

In QuickBooks Desktop, you have to create a file to upload to your state:

  • Choose Employees, followed by W-2s and Payroll Tax Forms, and then click Create State SUI E-file.
  • Then you have to select Continue twice.
  • Choose your state from the Select State drop-down menu.
  • After choosing Get QuickBooks Data, you have to click OK. 
  • Then you have to correct any errors or complete any missing data in the file.
  • Find the QuickBooks Payroll State SUI E-file drop-down menu on the Add-Ins tab, then click Start Interview.
  • Choose Next after selecting the I understand that I must review my data and respond to the following questions option.
  • Observe the location and file name. You will submit this file to the state. Click on Next.
  • You have to answer the questions and confirm all the details.
  • When the End of Interview window appears, choose Create State File by selecting Next.
  • Click OK.
  • To save the Excel workbook for your records, you have to select Yes. You will not send the state of this file.
  • Find the file QuickBooks saved for you in Step 8 and upload it to your state agency’s website.


  1. Does QuickBooks Desktop payroll pay all of the employee’s taxes?

    We can have us pay and file your federal and state payroll taxes for you, or you can do it yourself now.

  2. What is the best way to use QuickBooks Desktop for payroll?

    Step 1: Go to the Payroll tab in QuickBooks.
    Step 2: To begin, go to the top left of your screen and pick ‘Employees,’ then ‘Payroll Center,’ then ‘Pay Employees.’
    Step 3: Fill in the Payroll Data.
    Step 4: Create and Review Paychecks.
    Step 5: Verify your pay stub.

  3. What’s the best way to file payroll in QuickBooks?

    Keeping track of pay stubs-

    1. Your payroll service should be able to provide you with pay stubs or a payroll report for your employees.
    2. Choose + New.
    3. Select Journal Entry from the dropdown menu.
    4. Put the paycheck date in the Journal date box.
    5. Enter the paycheck number in the Journal no. area if you want to monitor it.

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