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Set up and manage Auto Payroll in QuickBooks Online Payroll

by Intuit•98• Updated 1 week ago

Learn how to set up and schedule payroll to run automatically with QuickBooks Online Payroll. Auto Payroll saves time by processing payroll each payday, so you don’t have to run it manually.

This article is for customers who use QuickBooks Online Core, Premium, or Elite Payroll.

Key things to know before using Auto Payroll

  • Bank holidays aren’t tracked – If a pay run falls on a bank holiday and employees need to be paid earlier, pause Auto Payroll and run payroll manually.
  • Email reminders – You’ll get notifications two business days before payroll runs and again once it’s processed.
  • Make changes before payroll – Adjust pay, deductions, or tax information before the payroll deadline.

Before you start:

  • Payroll setup must be complete and at least one payroll run processed.
  • Employees must have active status, salaried pay, and an assigned pay schedule.

To turn on Auto Payroll:

  1. Sign in to QuickBooks Online as the Primary Admin.
  2. Go to Settings Settings gear icon. and select Payroll settings.
  3. In the Auto Payroll section, select Edit ✎.
  4. Select Select employees for Auto Payroll and choose eligible employees.
  5. Select Save changes.
  6. Review the confirmation (employees and upcoming pay dates) and select Done.

What happens next?

  • You’ll get an email two business days before Auto Payroll runs with payday details.
  • After payroll is processed, you’ll receive another email confirmation.
  • Log in anytime to view or print payslips.

You can update employee pay, deductions, or tax details before payroll is processed.

To update payroll before it runs:

  1. Follow this link to complete the steps in product Open this link in a new window
  2. Select Run payroll. If multiple pay schedules exist, choose the correct one.
  3. Select Make updates to upcoming pay period.
  4. Find the employee to edit, select the Actions column (vertical ellipsis), then Edit payroll payment.
  5. Make the necessary changes and select Save.
  6. Select Save & preview Auto Payroll, then Save Auto Payroll.

If an employee on Auto Payroll needs a separate payment (e.g., bonus or adjustment), pause Auto Payroll for that pay period.

To pay an employee manually:

  1. Follow this link to complete the steps in product Open this link in a new window
  2. Select Run payroll.
  3. Select Pay manually this period for the relevant employee.
  4. (Optional) Add a note in the Memo column.
  5. To adjust hours:
    • In Actions, select Edit hours worked.
    • Choose Edit employee hours for this pay period, adjust hours in Reduce total hours by, then select Apply.
  6. Select Preview payroll, then Submit payroll.

Auto Payroll will resume automatically in the next pay period.

To stop Auto Payroll for one or more employees:

  1. Go to Settings Settings gear icon. and select Payroll settings.
  2. In the Auto Payroll section, select Edit ✎.
  3. Select Select employees for Auto Payroll and uncheck employees you want to remove.
  4. Select Save changes, review the confirmation, then select Done.
  • To keep payroll running smoothly, ensure all employee payments, tax filings, and required forms are up to date.
  • Regularly reviewing your payroll settings can help prevent last-minute issues.

What's next?

For more help, check out: