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Get started with Payroll

Learn how to set up and start using your new Payroll for QuickBooks Desktop or QuickBooks Online.

Payroll for Desktop or Online makes it easy to manage payroll, whether you choose to do it yourself, or let us do it for you.

Here's a handy guide for setting up your Payroll. We also put together essential info you need to get started with payroll tasks, from paying employees to taking care of taxes.

What you need before setting up Payroll

Here's the setup information you need for Desktop or Online Payroll. You can get this information from your previous payroll provider, your own records, your accountant, or from federal and state agencies.

You'll need your company bank account for direct deposit, or electronic tax payments.

  • Types of employee benefits: such as hourly wages, salaries, bonuses, commissions, and tips
  • Types of employee compensation: such as health and dental insurance, 401(k), retirement plans, vacation/sick leave, or Flexible Spending Account (FSA)
  • Other additions and deductions: such as cash advances, mileage and travel reimbursements, union dues, and wage garnishments
  • Completed Form W-4for each employee
  • Tip: If not available, enter "single" and "0" allowances. You can change these values later.
  • Pay rate: hourly, salary, commission, etc.
  • Paycheck deductions: employee contributions to health insurance, retirement plans, or garnishments (child/spousal support)
  • Pay schedule: weekly, bi-weekly, semi-monthly and monthly
  • Sick/vacation hours policy and balance: if applicable
  • Hire and termination date

You'll need your employees' bank account and routing numbers for direct deposits to their bank accounts (additional fees may apply depending on your product).

  • Federal Employer Identification Number (FEIN) and state agency ID numbers: You'll need unique ID numbers from the IRS and state agencies to file and pay taxes. Contact the agencies to apply for these ID numbers (see Federal and State payroll tax forms and resources).
  • Filing requirement and deposit schedule for payroll taxes: Requirements for when to file and deposit payroll taxes vary. Companies that owe more payroll tax typically pay and file more frequently. See Federal and State payroll tax forms and resources or contact the IRS and your state agency to determine your requirements.
  • Electronic Federal Tax Payment System (EFTPS) enrollment: It's mandatory to submit federal tax deposit payments electronically. You can enroll in EFTPS at You can learn more about EFTPS here.
    Note: If you have Assisted or Full Service Payroll, we'll submit the EFTPS enrollment on your behalf.
  • Other tax information: Such as state unemployment, assessment, surcharge, administrative or training tax rates, tax deposit schedules, and local or other taxes, if applicable.

If you've already paid employees this calendar year, we need to know the amounts to accurately calculate new paychecks and complete your tax forms.

  • For the current quarter: payroll details from each paycheck
  • For each prior quarter of this calendar year: summary by employee and summary for all employees (total company payroll)
  • Year to date totals for each employee: summary by employee
  • Year to date totals for each employee as of the last paycheck in the previous quarter: summary by employee
  • For the current quarter: copies of all payroll liability checks
  • For each prior quarter of this year: summary of payroll liability payments

Set up Payroll

Once you have all information you need, proceed to setting up your Payroll service.

If you have a Do it for You Payroll

QuickBooks Online Payroll Elite- we'll walk you through setting up your Payroll, or you can choose to have one of our Setup Experts do it for you.
 Intuit Full Service Payroll- we'll do most of the setup for you.

QuickBooks Desktop Assisted, QuickBooks Online Payroll Core, or QuickBooks Online Payroll Premium - we'll walk you through setting up your Payroll.

If you have a Do it Yourself Payroll

QuickBooks Desktop Basic or Enhanced, QuickBooks Online Payroll, Intuit Online Payroll-  we'll walk you through setting up the basics of your Payroll.

Payroll Subscription

Don't know which payroll service you're using? Find out which payroll service you have.

You can also upgrade or downgrade your payroll subscription. Here how:

Make sure to activate QuickBooks Desktop Payroll first before running the Payroll Setup Wizard.

Start Payroll Setup Wizard

  1. To set up your Payroll, open QuickBooks Desktop.
  2. Select the Employees tab in the top toolbar.
  3. Scroll and select Payroll Setup in the dropdown menu to open the wizard.
  4. Follow the Payroll Setup Wizard.

Start Payroll Setup Wizard

  1. To set up your Payroll, open QuickBooks Desktop.
  2. Select Employees tab in the top toolbar.
  3. Scroll and select Payroll Setup in the drop-down menu to open the wizard.
  4. Follow the Payroll Setup Wizard.

To activate your Payroll software, contact the Onboarding team at 800-365-9626.

Set up Enhanced Payroll in QuickBooks Online

  1. Go to the Payroll menu,  then select Employees.
  2. Select Get Started with Payroll to begin the setup process.
  3. Enter in company and employee information.  Use our Getting Started with Payroll tutorial page to help you with the setup process.
  1. Go to the Employees menu, then select Add Payroll.
  2. Select Try It Now to create a payroll account. If you already have one, select Current Customer Sign In to sign in to your account.
  3. Go to the To Do tab.
  4. If you haven’t already, select Complete Setup. If you’re ready to process payroll, select Run your first payroll.

You can sign up in QuickBooks Online, or contact our payroll sales department 877-683-3280.

Set up your payroll service with  QuickBooks Online Payroll Core, QuickBooks Online Payroll Premium, QuickBooks Online Payroll Elite and QuickBooks Online Payroll Full Service.

  1. Go to the  Payroll menu, then select Employees.
  2. Select Get Started with Payroll to begin the setup process.
  3. Enter in company, employee and tax information.
  4. Once completed, you will see a Run payroll button in your Employees screen.  If you don't see this, please contact our Onboarding team at 800-882-9900. You can also check out our Setting Up Full Service Payroll tutorial page to help you with the setup process.

Looking ahead

Done setting up your Payroll? Here's a quick overview of the most common tasks you'll need to complete this year.

Run payroll

With Desktop or Online Payroll, it’s easy to make sure everyone gets paid on time. Just enter your employees' hours, and we'll do the math for you. Each calculation is automated and accurate.

Pay and file federal and state taxes

Your Payroll monitors and updates your federal, state, and local taxes so you don't have to. You'll get helpful email reminders from us too, so your taxes and forms are always on time.

You can file forms and pay taxes electronically. Or, you can let us do it with Assisted or Full Service Payroll.

Prepare for the year-end

As the end of the year approaches, it's important not to miss any of the necessary tax activities. Staying on top of these changes can help you plan accordingly.

Update your tax tables (for QuickBooks Desktop users only)

Are you using QuickBooks Desktop Payroll Basic or Enhanced? We recommend that you update your tax tables at least every 45 days, or every time you pay your employees. If you have Online Payroll, your tax tables are updated automatically.

Learn how to update Payroll tax tables. You can also verify if you already have the latest tax tables.

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