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Set up payroll

Learn how to set up Payroll.

Are you setting up payroll for the first time in QuickBooks? These videos will give you an overview of the process. We also have a checklist and helpful links to get you started.


Company information

You need to have your  Employer Bank Account. You'll use this for direct deposits and electronic tax payments.

Note: If you plan to pay your employees using direct deposit, this service takes 5 business days to activate. You need to pay your employee by check first until your direct deposit is activated. Get help with all your Online Payroll direct deposit questions.

Company tax information

Make sure you have the following payroll tax information. You can get them from the IRS and your state local agency.

  • Federal Employer Identification Number and State Agency ID numbers: You need these unique ID numbers from IRS and state agencies to file and pay taxes. Contact IRS and your state agency to apply for these ID numbers.
  • Filing requirement and deposit schedule for payroll taxes: Requirements and dates to file and deposit payroll taxes vary. Companies that owe more payroll tax typically pay and file more frequently. Ensure you have the appropriate requirements and schedule for your company.
  • Other tax information: This includes state assessment, surcharge, administrative or training tax, and local or other taxes, if applicable.

Helpful Articles

Setup Scenario Helpful Links
  • Entering Federal EIN
  • Entering State ID Numbers
  • Entering Deposit and Filing Schedule
  • Entering SUI Rate

Employee information

Enter each employee you paid this calendar year (including active, inactive, and terminated employees). Make sure you have the following:

  • Completed Form W-4: for each employee
  • Pay rate: Hourly, Salary, commissions, etc
  • Paycheck Deductions: Employee contributions to health insurance, retirement plans, or garnishments such as child or spousal support
  • Sick or Vacation hours balance: If applicable
  • Hire and termination date

Helpful Articles

Setup Scenario Helpful Links
  • Completing Form W-4
  • Adding Pay type
  • Adding Paycheck Deductions
    (Voluntary deductions, retirement plans, garnishment)
  • Setting up for Direct Deposit
  • Set up Vacation/Sick Hours
  • Bonuses
  • Set up pay schedule

Payroll History

If you already paid your employees this calendar year, we need to know the amounts in order to accurately calculate your new paychecks and complete your tax forms. You can find this information on your employee pay stub or payroll reports.

Make sure to collect the following reports from your previous payroll provider:

  • Year to date totals for each employee
    • Gross Wages (by paytype)
    • Tax amounts (by paytype)
    • Deduction amounts (by deduction type, pretax and aftertax)
    • Net Pay
  • Year to date totals for each employee as of the last paycheck in the previous quarter
    • Gross Wages (by paytype)
    • Tax amounts (by paytype)
    • Deduction amounts (by deduction type, pretax and aftertax)
    • Net Pay
  • Payroll totals for the current quarter by pay date
    • Pay period and date
    • Gross wages (by paytype)
    • Tax amounts (by paytype)
    • Deduction amounts (by deduction type, pretax and aftertax)
    • Net pay
  • All tax payments paid this year
    • Type of tax payment
    • Total taxes paid
    • Date of payment

Helpful Articles

Setup Scenario Helpful Links
  • Entering Prior Payroll
  • Enter Prior Tax Payments

Run Payroll

If direct deposit isn't ready yet, print and give checks to your employees. You can print them on QuickBooks Online compatible pre-printed checks that you can purchase by:

It's recommended to use MICR (Magnetic Ink Character Recognition) toner or ink to print on blank check stock. This feature isn't currently offered to Intuit Online Payroll MAC users.

Helpful Articles

Setup Scenario Helpful Links
  • Setting up Direct deposit
  • Create Paychecks
  • Setting up Printing Preferences
  • Printing Pay stubs

Set up additional services

We have a list of articles to help you set up additional payroll services.

Setup Scenario Helpful Links
  • Electronic Services
  • Time Tracking
  • Worker's Compensation
  • Labor Compliance

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