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Get started with QuickBooks Desktop Payroll

SOLVEDby QuickBooksQuickBooks Desktop Payroll16Updated December 06, 2021

Learn the info needed and process behind how to set up your new QuickBooks Desktop Payroll Basic, Enhanced, or Assisted service.

Pay your team quickly, accurately, and on time with QuickBooks Desktop Payroll. You’ll need to complete a few tasks to get started.  Here’s a handy guide and videos to help you get set up.

Step 1: Activate your payroll subscription

Once you purchase your QuickBooks Desktop Payroll Basic or Enhanced Payroll annual subscription, you need to activate it.  The steps to activate depend on if you purchased it online, by phone, or from a retail store.

If you purchased QuickBooks Desktop Payroll Assisted, follow the steps in Enter your payroll service key.  Then you’ll activate your monthly payroll subscription at the end of the setup process with a QuickBooks expert.

If you purchased QuickBooks Desktop Payroll Basic, Enhanced, or Assisted online or by phone, you’ll receive a 16-digit service key by email.  You’ll enter this key in QuickBooks so you can use the payroll features. 

If you didn’t receive your service key, check your junk or spam folder, or use our automated Service Key Retrieval tool. You'll need to sign in using your Intuit Account login.

Enter your service key:

  1. Open your QuickBooks Desktop company file. 
  2. Select Employees, then Payroll, and then select Enter Payroll Service Key (or Manage Payroll Service key if you have a different payroll subscription). 
  3. Select Add (or Edit if a payroll service is already listed, then Remove payroll service key in QuickBooks Desktop before the next step). 
  4. Enter your service key
  5. Select Next, and then Finish
  6. When the Payroll Update message appears, select OK
  7. Verify your payroll service status is Active, and then select OK. 
  1. Open your QuickBooks Desktop company file. 
  2. Select Employees, then Payroll, and then select Install Payroll from Box.
  3. Enter the info in the Payroll License and Product Information page. You can find your license number on a brightly colored sticker on the folder inside the box.  The product number is in the directions on the folder. You’ll get a 16-digit service key to enter in during step 5. 
  4. Select Continue
  5. Follow the on-screen steps to complete your payroll activation, including entering your service key. 

Step 2: Complete the online application/create a Payroll PIN (QuickBooks Desktop Payroll Assisted only)

In this task, you’ll connect your bank account so you can use direct deposit and we can pay and file your payroll taxes.  

  • Your business legal name, address and Federal Employer Identification Number (FEIN)
  • Principal officer’s name, home address, Social Security Number and birth date (this is the authorized signer on your business bank account)
  • Your business bank account online User ID and password, or the routing and account number of the account you want to use for your direct deposits and payroll taxes. (We know entering this data may be scary. Read about the multiple layers of security we use to keep your data safe)
  1. Select Employees, then My Payroll Service, and then select Activate Assisted Payroll
  2. Follow the on-screen instructions and enter the information in the application wizard. 
  3. Create your payroll PIN.  Your PIN should be 8-12 characters, letters and numbers only (no special characters).  

Step 3: Complete your payroll setup tasks

In these tasks, you’ll add your employees, set up your federal and state payroll taxes, and enter any paychecks and tax payments you’ve already paid this year.

We know it takes time to get your payroll info into QuickBooks.  So the setup is designed to allow you to add info at your convenience and save as you go. 

If you use QuickBooks Desktop Payroll Assisted, you can get help from a setup expert to complete these tasks and activate your service. 

To get to the setup tasks: 

  1. Open your QuickBooks company file.
  2. Select Employees, then Payroll Setup

In this task, you’ll enter your employees’ info, and you can invite your employees to enter some of their own info through our free QuickBooks Workforce product if you use QuickBooks Desktop Payroll Basic or Enhanced.  

Info you’ll need for each employee:

  • Completed Form W-4 and any state equivalent forms if applicable
  • Hire date
  • Birth date
  • Pay rate
  • Any paycheck deductions such as contributions to insurance, retirement, or wage garnishments
  • Bank account or pay card info for direct deposit (if applicable)
  • Sick, vacation, PTO accrual rates and balance (if applicable)

Check out this video to learn how to add your employees:

In this task, you can select from a preset list of pay items, insurance benefits and retirement deductions, or you can set up customer items.  If you offer your employees paid vacation and/or sick time off, you can add those too. 

Once you’ve set up your payroll items and time off, you can use the Assign to employees button to apply the items to multiple employees at once. 

Watch this video to learn how to set up your company items:

In this task, you’ll add your federal and state payroll tax info. If you use QuickBooks Desktop Payroll Enhanced, you can also set up to pay your payroll taxes electronically. 

Info you’ll need:

  • Federal Employer Identification Number (FEIN)
  • State Withholding and/or Unemployment account numbers: Contact your state agencies to register
  • Federal and state deposit frequencies:  how often you are required by the IRS and state to pay your taxes
  • State tax rates: Unemployment, surcharges, state disability, paid family leave, etc.

Check out this video to learn how to set up your payroll taxes

If you've already paid employees this year, you'll need to add those paychecks and any tax payments you've made.  This info is included on your employees’ W-2s at the end of the year. 

If you haven’t paid employees yet this year, you won’t need to complete this step. 

Info you’ll need:

  • Pay stubs or payroll reports for each of your employees paid this year (including any no longer with your business) 
  • Tax liability reports or tax payment receipts or statements

Check out this video to learn how to add your pay history

Check out this video to learn how to enter tax payments you've made this year

In this task, if you entered pay history, you’ll enter federal and state tax filing details for closed quarters.  QuickBooks will review all the pay history info and check for errors.  This ensures your employees’ W-2s are correct at the end of the year. 

Info you’ll need: 

  • Quarterly federal and state payroll tax forms for closed quarters (941, State Unemployment Insurance, etc)

Step 4: Activate your payroll service and sign your payroll authorization forms (QuickBooks Desktop Payroll Assisted only)

Once you’ve completed your setup tasks, contact us and a setup expert will review your setup to make sure everything is set up correctly for you to start creating paychecks.  Then they’ll help you activate your service.

Once you’re active, we’ll send the principal officer an email with payroll authorization forms attached.  These forms need to be signed by the principal officer and sent back to us as soon as possible so we can pay your taxes and file your forms. 

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