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Creating Payroll in QuickBooks Online

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QuickBooks Online can be your jack of all trades when it comes to your business. Invoicing? Check. Bills? Check. Inventory? Check! And it doesn’t stop there. Let’s take a look at one of the most important parts of your business….Payroll. In QuickBooks Online, it doesn’t have to be difficult to set up. We can help with A through Z!


All versions of our payroll options include these features:

  • Full-service payroll (including automated taxes and forms)
  • 1099 e-file/pay
  • Expert product support
  • Direct deposit


Before we start, let me explain what information you should have on hand in order to make this as quick as possible. You can get these from your previous payroll provider, personal records, accountant, or federal/state agencies:


  • Company bank information - for direct deposit and electronic tax payments
  • Compensation/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
  • Employees - W-4 form, pay rate, deductions, schedule, PTO, hire date
  • Direct deposit information - employee’s bank account and routing numbers
  • Tax information
    • Federal Employer Identification Number (FEIN) and state agency ID numbers: 
    • Filing requirement and deposit schedule for payroll taxes: See Federal and State payroll tax forms and resources or contact the IRS 
    • Electronic Federal Tax Payment System (EFTPS) enrollment: Mandatory. If you have Assisted or Full Service Payroll, we'll submit the EFTPS enrollment on your behalf.
    • Other tax information: Examples are state unemployment, assessment, surcharge, administrative or training tax rates, tax deposit schedules, and local or other taxes (if it applies to you).
  • Prior payrolls - 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.
  • Liability Information 
    • For the current quarter: copies of all payroll liability checks
    • For each prior quarter of this year: summary of payroll liability payments


OK, now let’s take a deep breath. Not only is that a lot of information, but some of you with a large number of employees may be particularly overwhelmed. Don’t worry, there’s no reason this needs to happen all in one day or session. Try breaking it up across the week, doing a bit at a time until you have everything you need. Maybe gathering payroll information one day, then focusing on taxes the next couple of days.


Once you have all your information gathered, next you just need to enter it into your account. 


  1. Go to the  Payroll menu, then select Employees.
  2. Select Get Started with Payroll to begin the setup process.
  3. Enter in the company, employee, and tax information.


Congratulations, now you’re in the home stretch! Entering all that information into your account is the backbone of a smooth payroll process. Now that everything is entered you’re ready to pay your employees:


  1. Go to the Payroll menu, then select Run payroll.
  2. Select a pay schedule, then Continue.
  3. Select the employees you want to pay.
  4. Check for the correct bank account, pay period, and pay date. Make changes as needed.
  5. Choose the employees’ pay method. *Note: If you choose “direct deposit” make sure that the employee’s direct deposit information is set up in their profile. If it isn’t, you can click on the employee’s name on this screen to set it up.
  6. Enter the number of hours worked.
  7. Hide or show pay types by selecting the Settings icon below the TOTAL PAY.
  8. Select Preview Payroll.
  9. To edit or preview a specific check, select the Edit (pencil icon) next to the check's net pay, then select OK when done.
  10. When you're ready, select Submit payroll.
  11. And there you have it! To print paychecks, select Print paychecks, then Finish payroll.


Phew, you did it! Payroll from here on out will be smooth sailing. As always, we always have your back here in the Community with any questions you have.


Check out these articles for a look into the ins and outs of payroll:


Prefer some visuals? Here is our library for payroll videos:

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