Set up and manage your Auto Payroll in QuickBooks Online Payroll

Learn how to set up and schedule your payroll to run automatically with QuickBooks Online Payroll.

You can save time running payroll each payday with Auto Payroll. If all or even some of your team is salaried or hourly and works the same amount of hours each pay period, Auto Payroll will create your paychecks automatically. Payday becomes one less thing for you to remember in your busy schedule. And it works if you pay your employees with paper checks or direct deposit. 

For a better experience, open this article in QuickBooks Online. Launch side-by-side view

We’ll show you how to:

• Set up Auto Payroll
• Make changes for the upcoming Auto Payroll
• Pay your employee manually
• Turn off Auto Payroll

This feature isn’t available in QuickBooks Desktop Payroll.

Set up Auto Payroll

To use Auto Payroll, you need to have completed your payroll setup and run your first payroll.

Check out the video on how to set up Auto Payroll in QuickBooks Online Payroll.

Step 1: Set up your employees

Make sure the employees you want to use Auto Payroll for are set up with the following:

• Employment status is Active
• Salary pay or an hourly rate with default hours
• A pay schedule
• Tax info (W-4 and state taxes)

Auto Payroll doesn’t work for commission-only employees, inactive employees, or 1099 contractors. We don’t recommend using it for hourly employees whose hours change each pay period.

To set default hours:

1. Go to Payroll, then Employees (Take me there).
2. Select your employee.
3. From Pay types, select Start or Edit.
4. Enter the Hours per day and Days per week.
5. Select Save, then Done.

Step 2: Turn on Auto Payroll

Sign in to QuickBooks Online as the Primary Admin, then choose which employees you want to pay with Auto Payroll.

1. Go to Settings and select Payroll settings.
2. In the Auto Payroll box, select Edit ✎.
3. Select the employees you wish to pay on Auto Payroll. You'll only be able to select eligible employees.
4. Select Save changes.
5. Review the confirmation display for the total number of employees and important dates related to your Auto Payroll processing.
6. Select Done.

Once your employees are enrolled, you’ll receive an email with the details of your upcoming payday, 2 business days before Auto Payroll processes. Then we’ll email you again after your Auto Payroll has been processed. You can sign in to QuickBooks Online to view or print paychecks.

Manage your Auto Payroll

Make changes for the upcoming Auto Payroll

Before auto payroll processes your payroll checks, you can make some changes with your employee’s pay info, deduction or contribution amounts, or tax info as needed.

You can make your changes 3 business days prior to the check date, until 5 PM PT. 2 business days before Auto Payroll processes your payroll checks, we email you the details and timing for your upcoming payday. If you missed making changes and the auto payroll has been submitted, contact us for help.

If this is a one-time change for the upcoming pay period:

1. Go to Payroll, then select Employees (Take me there).
2. Select Run payroll.
3. Select Make updates to upcoming pay period.
4. Select Actions ⋮, then Edit paycheck.
5. Edit the payroll items, then Save.
6. Select Save & preview Auto Payroll.
7. Select Save Auto Payroll.

Pay your employee manually

If your employee is currently enrolled in Auto Payroll and you need to pay them outside your normal payroll schedule, you can pause Auto Payroll for a pay period. Auto Payroll will start again on your next pay run.

1. Go to Payroll, then Employees (Take me there).
2. Select Run payroll.
3. Select Pay manually this period on the employees, you wish to pay manually.
4. Enter the date, pay schedule, and edit any pay items for this payroll.
5. Select Preview payroll and then Submit payroll.

Turn off Auto Payroll

If you wish to stop paying one or more of your employees via Auto Payroll, you need to unenroll them.

Make sure you're signed in to QuickBooks Online as the primary admin.

1. Go to Settings and select Payroll settings.
2. In the Auto Payroll box, select Edit ✎.
3. Select Select employees for Auto Payroll.
4. Select one or more of the enrolled employees.
5. Select Save changes.
6. Review the confirmation window, then select Done.