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 paycheques automatically. Payday becomes one less thing for you to remember in your busy schedule. And it works if you pay your employees with paper cheques or direct deposit. 

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.

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 (T4 and provincial 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.

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

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.

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 and select Employees (Take me there).
2. Select Run payroll.
   Note: If there are multiple pay schedules, select the one you want.
3. Select Make updates to upcoming pay period.
4. From the Actions column, select, then Edit paycheque.
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 and select Employees (Take me there).
2. Select Run payroll.
   Note: If there are multiple pay schedules, select the one you want.
3. Select Pay manually this period on the employees, you wish to pay manually.
4. Optionally, to add a memo, select + from the Memo column, enter your notes, and select Save.
5. To reduce employee hours,
   1. From the Actions column, select, then select Edit hours worked.
   2. Select Edit employee hours for this pay period and enter the hours in the Reduce total hours by box.
   3. Select Apply.
6. 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. Select Settings ⚙, then 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.