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How to manage Auto Payroll in QuickBooks

Manage Auto Payroll in QuickBooks

What is Auto Payroll in QuickBooks and how does it work?

QuickBooks Auto Payroll is a cloud-based payroll software that enables businesses to pay employees, file payroll taxes, and manage employee benefits and HR all from one location. The software saves time by automatically calculating, submitting, and paying federal and state payroll taxes.

After you’ve set everything up, you’ll be able to process Auto payroll in QuickBooks for your employees automatically. You can also do payroll manually from your PC or through the mobile app if you don’t like the automatic alternative. You can also incorporate deductions and contributions, multiple work sites, and paid time off in your reports.

How to manage Auto Payroll in QuickBooks Online

Consider adding QuickBooks Auto Payroll to your package if you already use QuickBooks Online and need to pay employees. It can be accessed from the same system that you use to keep track of your company’s finances, allowing for a smooth transfer of payroll expenses to the appropriate general ledger accounts.

Step-1:  Go to the “Auto Payroll” tab

  • You can set up payroll with QuickBooks Online and process your first pay run in just a few simple steps.
  • If you subscribe to a QuickBooks Payroll plan, you can even handle payroll as often as you need at no extra cost.
  • Furthermore, when you add QuickBooks Auto Payroll to your existing QuickBooks Online subscription and capabilities.

Step 2: Enter Paying Your Employee’s General Information

  • The system will next inquire if you have already paid staff this calendar year.
  • You must select “Yes” if you’re transferring from a manual system or another payroll software to QuickBooks Auto Payroll.
  • Note that later in the setup, the system will want you to provide year-to-date (YTD) salary details and tax payments made for each employee. 
  • You can get YTD data for each employee from the most recent payroll you processed. 
  • Aside from payments to employees for the current calendar year, the system will ask you when you plan to execute your first QuickBooks Auto payroll.

Step 3: Choose Employees’ Names In QuickBooks Auto payroll

  • After you’ve entered your workplace, a new window will emerge, allowing you to enter the basic information and payroll details for your employees. 
  • Start adding the required data for each Employee member on your payroll by clicking the “Add an employee” button.

Step 4: Select Information about the Employee In QuickBooks Auto payroll

  • You have the option of adding your employees’ email addresses in QuickBooks Auto Payroll.
  • This permits the system to send them a link to check their pay stubs online using QuickBooks Auto payroll Workforce, the provider’s self-service portal.

Step 5: Select “Run Auto Payroll” in Quickbooks

  • Click the “Run Payroll” button in the right-hand corner of the screen on your “Payroll” dashboard.

Step 6: Make a note of the current hours in the Auto payroll

  • Enter the actual hours worked for all hourly employees in the “Regular Pay Hrs.” column, then double-check the rest of the data for correctness.
  • Select the “Preview Payroll” button in the bottom right corner once you’re done.

Step 7: Examine and Submit Your Auto Payroll in QuickBooks

  • Check the payment method to confirm that employees who direct deposits and paychecks should pay to show up correctly.
  • Aside from the total hours worked and other payment details.
  • Also, double-check the tax amounts for both the employer and the employee.

Manage  Auto Payroll in QuickBooks

In QuickBooks Online Payroll Core, QuickBooks Online Payroll Premium, or QuickBooks Online Payroll Elite, learn how to make temporary or permanent modifications to your Auto Payroll.

You may need to make modifications to your Auto Payroll as circumstances change with your employees or company. Look for an email with the subject Your QuickBooks Auto Payroll preview at the beginning of each pay period.

The preview summary shows the total amount of your payroll as well as the total number of employees who have been paid. Follow the procedures below to make changes to your employees or payroll. In your email, you’ll have a deadline for making the modifications.

1. Make a one-time modification to your employee’s Payroll info

  • Choose Payroll.
  • Select Payroll Run
  • Select Update Auto Payroll from the drop-down menu.
  • Select Done after making any necessary changes to the paychecks.

2. Make a permanent modification to your employee’s Payroll info

  • Go to Employees, then to Payroll.
  • Choose your employee.
  • Make any necessary changes to your compensation, deductions, and W-4 info.
  • Select save when you’re done.

3. Pay your employee Manually

You can halt Auto Payroll for a pay period if your employee is currently enrolled in it and you need to pay them outside of your normal payroll schedule. On your next pay run, Auto Payroll will begin again.

  • Payroll is selected, and then Payroll is run.
  • On the employees, you want to pay manually this period, select Pay manually this period.
  • For this payroll, enter the date, pay schedule, and any pay items that need to be changed.
  • Choose Preview and then Submit.

4. Activate Auto Payroll in QuickBooks

You must unenroll one or more of your employees if you want to stop paying them through Auto Payroll.

Make sure you’re logged in as the primary admin in QuickBooks Online.

  • Select Payroll Settings from the drop-down menu under Settings.
  • Select Edit in the Auto Payroll box.
  • Select Manage Auto Payroll from the drop-down menu.
  • Choose one or more of the employees who have been enrolled.
  • Select the Save Changes option.
  • After reviewing the confirmation window, click Done.


If you create hourly employees without default hours, your Auto Payroll in QuickBooks may become inactive. If this happens, you’ll receive an email from the payroll administrator, and you’ll need to make and send your payroll as usual.


  1. In QuickBooks, what are Auto-payroll items?

    The Payroll Item list is the name of this list. Compensation, taxes, additional additions and deductions, and employer-paid expenses are all included in the payroll. Payroll items are used by QuickBooks to monitor individual pay cheque amounts as well as year-to-date wage and tax amounts for each employee.

  2. What is the purpose of Auto-payroll in Quickbooks?

    Acknowledging Payroll in QuickBooks

    Auto Payroll is the process of paying a company’s employees, which involves keeping track of hours worked, calculating pay, and disbursing funds to employees via direct deposit or check.

  3. What is the best way to enter Auto-payroll items into QuickBooks?

    1. Select Lists > Payroll Item List from the QuickBooks Desktop options at the top.
    2. Select the Payroll Item button > New in the lower-left corner of the Auto Payroll Item List.
    3. Select Custom Setup before moving on to the next step. Choose Wage, then Next.

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