Here's everything you need to know when setting up your employee's payroll in QuickBooks. You can also find information about paying employees, paying federal and state taxes, and filing tax forms.

Payroll setup checklist

You'll need the following information to set up your desktop or online payroll account. You can find the information from your previous payroll provider, in your own records, from your accountant, or from federal and state agencies.

1. Company Information

  • Company bank account: For direct deposit or electronic tax payments.

2. Compensation and Benefits

  • 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.

3. Employees

  • Completed Form W-4 for 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 dates.

4. Direct Deposit

  • Direct Deposit: Employees' bank account and routing numbers for direct deposits to their bank accounts (additional fees may apply depending on your product).

5. Tax Information

  • 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 www.eftps.gov/eftps.
  • Other tax information: Such as state unemployment, assessment, surcharge, administrative or training tax rates, tax deposit schedules, and local or other taxes, if applicable.

6. Prior Payrolls

NOTE: 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

7. Liability Information

  • For the current quarter: Copies of all payroll liability checks.
  • For each prior quarter of this year: Summary of payroll liability payments.

Getting started with Payroll/Setup payroll

QuickBooks Desktop Payroll Basic or Enhanced

QuickBooks Desktop Payroll Assisted

To activate QuickBooks Desktop Payroll:

  • 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 dropdown menu to open the wizard.
  • Follow the Payroll Setup Wizard. 

Note: To activate your Payroll software you will need to contact our Onboarding team at 800-365-9626

QuickBooks Online Payroll

  • Sign-up
  • Setup process
    1. Select Workers from the navigational menu then select Employees.
    2. Select Get set up 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.

Quickbooks Online Payroll Full Service

  • Sign-up
  • Setup process
    1. Select Workers from the navigational 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 do not see this, please contact our Onboarding team team at 800-882-9900. You can also review our Setting Up Full Service Payroll tutorial page to help you with the setup process.

Looking ahead

Here's a guide to the most common tasks you'll need to complete this year.

Running Payroll

To pay your employees:

QuickBooks Desktop Payroll Basic or Enhanced Quickbooks Desktop Payroll Assisted QuickBooks Online Payroll QuickBooks Online Payroll Full Service Intuit Online Payroll  Intuit Full Service Payroll
Create paychecks Create paychecks Create paychecks Create paychecks Create paychecks Create paychecks

All products: For holiday payroll processing, see How will Christmas Day and other federal holidays affect my payroll processing?

For QuickBooks Desktop Payroll Basic, Enhanced, and Assisted only: Intuit recommends that you update your tax tables every time you pay your employees, or at least every 45 days.

Pay Federal and State taxes

Intuit's goal is to make your tax filing as simple as possible so that you can focus on running your business.

QuickBooks Desktop Payroll Basic or Enhanced Quickbooks Desktop Payroll Assisted QuickBooks Online Payroll QuickBooks Online Payroll Full Service Intuit Online Payroll  Intuit Full Service Payroll
E-file and E-pay: General Info Assisted Quick Tax Guide Pay liability taxes with e-pay or check Access payroll tax forms and tax payments Pay liability taxes with e-pay or check Access payroll tax forms and tax payments

Filing quarterly tax forms

Intuit Payroll helps you generate and file your tax forms by:

  • Interviewing you and asking questions about your business and employees
  • Auto-populating forms wherever possible using information you provide
  • Automatically generating your tax forms
  • Quickbooks Desktop Payroll Assisted, Quickbooks Online Payroll Full Service, and Intuit Full Service Payroll files your state and federal filings for you
QuickBooks Desktop Payroll Basic or Enhanced Quickbooks Desktop Payroll Assisted QuickBooks Online Payroll Quickbooks Online Payroll Full Service Intuit Online Payroll  Intuit Full Service Payroll
E-file and E-pay: General Info Assisted Quick Tax Guide File tax forms overview Access payroll tax forms and tax payments Filing for federal and state taxes Access payroll tax forms and tax payments

Year End

QuickBooks Desktop Payroll Basic or Enhanced Quickbooks Desktop Payroll Assisted QuickBooks Online Payroll QuickBooks Online Payroll Full Service Intuit Online Payroll  Intuit Full Service Payroll
Year End Center: QuickBooks Desktop Payroll Basic, Standard, & Enhanced Year End Center: QuickBooks Desktop Payroll Assisted Year End Center: QuickBooks Online Payroll Enhanced Year End Center: QuickBooks Online Payroll Full Service Year End Center: Intuit Online Payroll Basic & Enhanced Year End Center: Intuit Full Service payroll

Additional topics

Intuit QuickBooks Desktop Payroll Basic, Standard,& Enhanced  Learn & Support site
Intuit QuickBooks Desktop Payroll Assisted Learn & Support site
Intuit QuickBooks Online Payroll Full Service Learn & Support site
Intuit Online Payroll Learn & Support site
Intuit Full Service Payroll Learn & Support site