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Interested in QuickBooks Online Automatic Payroll?

If you have all salaried employees on direct deposit (more eligibility criteria below)* with QuickBooks Online Payroll’s Auto Payroll feature you will be able to run your payroll automatically so your employees are paid on time every pay period without you having to sign in.


Here’s how it works:



Once Auto Payroll is enabled:


1.  4 business days before payday - You receive a brief payroll summary (including pay period, number of employees being paid, and payroll amount) sent to your email. You can sign in to QuickBooks Online Payroll to view a Preview Payroll Details report, by employee, if you wish.


2.  3 business days before payday - Make any changes to your Auto Payroll by 5 PM PT.


3.  On payday - Money is  automatically withdrawn from your bank account and employees are paid on time, as long as you continue to meet eligibility requirements.


Here's how to enable Auto Payroll


You can enable Auto Payroll from one of three places in the product:


1.  Overview page:  In the "STATUS" box, select "Learn More" and follow the prompts



2.  At the end of Run Payroll flow: Click on "Check out Auto Payroll" and follow the prompts    


3. Payroll Settings: Select Gear icon -> Payroll Settings.  Toggle to On and follow the prompts





To make changes to Auto Payroll
You can make two types of changes to your Auto Payroll pay run:


1. One-time change: To make a one-time change, for one pay run only, ( bonus or reimbursement as a pay type) before the change deadline (noted in the preview email and on your Overview screen), below are two ways in which you can make these changes:


  • Select: Run payroll > Review or update Auto Payroll, and make one time updates for this pay run only:
  • Or select Update Auto Payroll:

2. Recurring change: To make a change that is permanent and remains across future pay runs (e.g. salary update or deduction changes), go to Employees > select the employee, and make the change before the deadline.



To pay an employee manually

Select Run Payroll > Run payroll manually. We won’t create duplicate paychecks for anyone you pay through this manual pay run. Auto Payroll will start again with your next pay run.


Cancel Auto Payroll 

You can cancel Auto Payroll anytime before the edit deadline (in the example above Tuesday at 5 PM PT) in ‘Payroll Settings’. You will be responsible for running payroll manually on time to meet your payday after turning off Auto Payroll.


To skip paying an employee while using Auto Payroll: Edit the employee and make them inactive.


*Eligibility criteria 

  • All salaried employees
  • All employees on direct deposit
  • Single pay schedule
  • Setup fully complete and E-services enabled
  • No insufficient funds hold in the last 6 months
  • Commission only paychecks (no salary, only commission)

Important Notes:

  • As the employer, you will be responsible for making any changes before the edit deadline should any of your employees go on vacation, leave the company, or if anything else changes with your business. This helps us make sure we automatically withdraw the correct amount to pay your team and can keep you from mistakenly overpaying your employees.
  • Updating Auto Payroll is not permanent. For example, if you update Auto Payroll for a reimbursement or deduction, the amount is only for that pay run. If you update a reimbursement or deduction when editing the Employee, that change is permanent for all future pay runs.
  • Reminder emails go to the Payroll Admin. To change this, go to Gear icon > Payroll Settings > Email and make changes there.
  • Changes which will make Auto Payroll inactive: Creating Hourly employee, or changing their pay preference to check. If your account changes and are no longer eligible for Auto Payroll, the Payroll Admin will receive an email, and you are responsible for all subsequent payrolls.



Please send an email to if you have any questions.
Spots are limited, so be sure to enable Auto Payroll as soon as you have a chance.