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Auto Payroll

Turn on and manage Auto Payroll

Auto Payroll is a feature that allows you to process your payroll automatically without logging in to QuickBooks Online Payroll. You can save the planning and time it takes to pay your employees by using Auto Payroll.


Note: Auto Payroll does not exist for contractor payments. Please continue the regular workflow for Contractor payments.


Criteria for Auto Payroll

Make sure your QuickBooks Online Payroll meets following criteria:

o  You have Full Service (available for most companies), Core, Premium or Elite payroll

o  All employees are either salaried or have default hours set

o  All employees are on a single pay schedule

o  Payroll setup is fully complete

o  First payroll has been run


Enable Auto Payroll

 If above criteria is met, you will be able to enable Auto Payroll

  1. Select Gear ⚙ icon on top right, and go to Payroll Settings
  2. In the Auto Payroll box, turn on Auto Payroll
  3. Select Save

Note: You are also able to enable Auto Payroll from the Overview page status box (mid right side) or after running payroll on the Finish page.


Here's how it works:

To understand how Auto Payroll will work, there are couple important items to remember: 

  1. Pay date: This is the day when your employees will get paid
  2. Money movement lead time: This is the number of days before pay date net pay funds will be debited from your bank account by Intuit. Money movement lead time could be the same day (day of pay date) or 5 days depending on your specific situation.  If your employees are not set up with Direct Deposit, you will need to log into QuickBooks Online Payroll to print the checks. 

Every pay period: 

  • You will receive a preview summary of your payroll early in the pay period (please see the Welcome email sent by Auto Payroll to know your exact first time dates. After the first time, the timeline will remain consistent). 
  • After you receive the preview summary, you will have 1-2 business days to review and make any changes to your payroll (exact cut-off time for changes to be submitted will be stated in the preview summary email)
  • Paychecks will be created by Auto Payroll after the cut-off time. 
  • Funds, for your employees on Direct Deposit,  will be debited from your account according to your money movement lead time (please see what your lead time is in Payroll Settings). 
  • On Payday, your employees on Direct Deposit will get paid automatically. You will have to log in to QuickBooks Online Payroll  and print checks for those of your employees getting paid using paper checks. 

Manage your Auto Payroll

Once you have turned on your Auto Payroll, there are few things to keep in mind before payroll runs.

If one of your employees leaves the company or takes some time off, or something changes with your company, you'll need to make changes to your payroll.

Note: You can find your lead time and deadline to edit your payroll in your brief payroll summary email


Make a one-time change

  1. Select Run payroll, then Update Auto Payroll
  2. Edit any fields to update that paycheck.
  3. Select Done.

Updating your employees' payroll (recurring change)

  1. Go to Employees, and select the employee.
  2.  Make the change before the deadline.
  3. Change any employee setting such as salary, deductions, default hours etc.
  4. Select Done.

Pay an employee manually

If you need to pay your employee with an off schedule payroll, you can pause Auto Payroll for a pay period and pay your employee manually. Auto Payroll will start again with your next pay run.

  1. Select Run Payroll, and then Run payroll manually
  2. Enter the date, pay schedule, and edit any pay items for this payroll.
  3. Select Preview and then Submit

Turn off Auto Payroll for an employee or altogether 

Ensure that you turn off Auto Payroll before the paychecks are created for the current pay cycle (which happens after the cut-off date, stated in the preview email)

If you want to stop paying an employee via Auto Payroll, you need to make them inactive.

  1. Go to Employees, and select the employee.
  2.  Make the change before the deadline.
  3. Change the employee's status to: Not on Payroll or Terminated.
  4. Select Done.

Be on the lookout for emails and text messages

If something needs to be updated and addressed with your Auto Payroll, you'll receive an email and text messages from Intuit.

If you subscribed to text messages for Auto Payroll and wish to unsubscribe, please text STOP to 87027. For additional customer support, please 1-800-4Intuit.

*If you have TSheets or other tools for getting hours, those hours will get a priority relative to the default hours that are setup in the system. 


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 without Default Hours, or adding a new payroll schedule. 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.
Best answer August 15, 2019

Best Answers

Auto Payroll

Do you have a group of salaried employees that are all on direct deposit? We are still looking for customers that would like to try early access to QuickBooks Payroll Auto Payroll. Check out this article above if you're interested in signing up or just want to read more about it.

View solution in original post

5 Comments 5

Auto Payroll

Do you have a group of salaried employees that are all on direct deposit? We are still looking for customers that would like to try early access to QuickBooks Payroll Auto Payroll. Check out this article above if you're interested in signing up or just want to read more about it.

View solution in original post

Level 2

Auto Payroll

The only reason I cannot enable this function is what *might* be a typo in the interface, but I cannot trust it.



At one point in the past I had an Axos Business Checking account attached.  That account has long since been removed, but I cannot find a way to get QuickBooks to completely "forget" it ever existed.


I now have an account that also happens to start with an "A".  It's what should be used for payroll.

The Auto Payroll setup window shows this:AutoPayroll.png

Problem is, the last 4 are correct, but that's not an Axos bank, it's the other one.

When I go in to manually run, it has Axos in the list selected and gives the message basically "yeah, but whatever you put in Settings, that's what we'll use" - great, but I need the interface to tell me WHICH account it's using, correctly.


I suspect if I can get QuickBooks to completely "forget" about Axos, it solves the problem and reassures me.  But despite my every effort I can't figure that out.


If I could solve that, I would be open to this function.

QuickBooks Team

Auto Payroll

Thanks for the response, @megasolutionsllc.


To make changes to your bank account you have on file for your Full-Service Payroll in QuickBooks Online, then you'll have to reach out to our Payroll Support. Rest assured, they have the tools that can pull up your Payroll information and help make changes to your account. This is so that you have the correct bank account for your Tax Payments and Payroll Transactions.


You can let me know how the conversation goes by leaving me a Reply. I'll be here if you need anything else. Have a beautiful day.

Level 2

Auto Payroll

You didn't read my post.


The bank account is correct in Settings.  The account NUMBER shown is correct.  It's the account NAME that's wrong.

This is an interface issue.  But it means I can't trust auto because I can't know if it's truly going to try to ping that account (by name) vs. the right account (by number).


What I am saying, is that my screenshot should be sent to the developers to fix it.

QuickBooks Team

Auto Payroll

Hello there, megasolutionsllc.


Thanks for getting back and making things clear to us.


I'll make sure to take note of this and inform our developers about this feedback. 


For future reference, you can also run reports for specific accounts in QuickBooks Online (QBO): Run Reports in QBO.


You can touch base with us if you have any other concerns. I'll always be around to help.

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