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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. You can now choose which employees should get paid automatically - one employee, some employees, or all of your employees.


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  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 one or more people from your employee list. You can only select employees that are eligible for Auto Payroll.
  4. Select Save Changes

Note: You can also enable Auto Payroll from the Overview page or after running payroll from the Finish Payroll 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)
  • For employees not enrolled in Auto Payroll, run payroll manually
  • 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
  2. Select Make an Update
  3. Edit any fields to update the paycheck.
  4. Select Done.


Updating your employees' payroll (recurring change)

  1. Make the change before the cut off deadline
  2. Go to Employees, select he employee
  3. Edit any fields such as salary, default hours, deductions, 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,
  2. Employees who will be paid automatically appear with a status of "Enrolled".  For each employee enrolled, select Pay manually this pay period.  The employee status will change to reflect "Enrolled. Manual Run".  To change an employee back to pay automatically, select Manual Run, then Pay automatically this period.
  3. For each employee, edit any pay items for this payroll.
  4. 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 unenroll them.

If you unenroll all your employees, Auto Payroll will be turned off completely.

  1. Select the Gear icon, and go to Payroll Settings.
  2. In the Auto Payroll section, select the Edit icon.
  3. In the Setup Auto Payroll section, select Manage Auto Payroll.
  4. Select the enrolled employees. Their status will change to "Not Enrolled".
  5. Select Save Changes.
  6. Review the confirmation of how many employees are enrolled in Auto Payroll as well as when automatic payments will process.
  7. 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, choose Help in QuickBooks for more targeted support or 1-800-4Intuit.


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.

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.

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.

Ashley H
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.

Level 2

Auto Payroll

Does automatic payroll feature also automatically e-pay payroll taxes?  You may want to make this clear when you sign people up to avoid confusion.

QuickBooks Team

Auto Payroll

I can clear things out for you, vassili-gorshkov.


Yes, the Auto Payroll feature allows us to e-pay taxes automatically. We pay and file your returns for you in QuickBooks Online.


If you haven't set up this function, you can visit this link for instructions and detailed steps: Use Auto Payroll to pay your employees.


If you need assistance in setting up the Auto Payroll on your account, you can chat with our Support Team.


Please visit this page to select our product and fill out the form to get in touch with an expert: Contact Payroll Support. Select QuickBooks Online and click the link for your payroll plan.


Let me know if you have follow-up questions about the feature by commenting below. I'm always right here to help.

Level 1

Auto Payroll

hello I need help for my payroll



QuickBooks Team

Auto Payroll

Welcome to the Community, orgilbattulga.

I want to ensure I can provide the best solution to your payroll concern. To get on the same page, I need to gather some information.

What area in the payroll service do you need help with? Did you encounter any errors when processing payroll?

I appreciate any details you can provide. Looking forward to working with you again. Have a good one. 

Level 1

Auto Payroll

I am not happy with Quick books online "AUTO" payroll. The interface is awful. The QB Desktop version is way easier to use and does not have all the glitches.  "What glitches?", you might ask, well the glitch that it cannot accept hours from part time employees who fill different shifts during a week.  SO, its NOT actually an AUTO payroll. HOW many companies pay employees exactly the same every week??  Few. SO, Why is this a requirement to have "AUTOPAY"?? because "autopay" can't handle getting the hours from t-sheets and paying them for whatever times the employees work. THIS IS NOT AUTOPAY> I THINK you should qualify the AUTOPAY feature in your SALES pitches since this is the SINGULAR REASON I SWITCHED FROM DESKTOP>   I am NOT HAPPY AT ALL.  Your costs are astronomical, payments are deducted with no discussion. once QUOL has your bank details, you can't stop them from taking their "auto deductions"  - and not least of my complaints is that your service is the WORST... you cannot get hold of a real person, certainly not on the phone, and the chat "HELP" careless and the information is almost always a LINK to self help or the FAQs... SO FRUSTRATING. There is NONONE to talk to about the bank debits, no one will ever discuss a refund. I am sick that I purchased this software. I wish I had never even tried to move from DESKTOP.

Level 1

Auto Payroll

In need help I can’t login to my account it says refresh your screen it’s nothing working what do I do
Candice C
QuickBooks Team

Auto Payroll

Good morning, @Christinewiltz


Thanks for joining in on this thread. I hope your week is going well so far. 


Since you've tried refreshing the page and the issue is persisting, I recommend contacting our Customer Support Team. They'll be able to use more advanced tools to look further into your account to help you out. Here's how: 


  1. Go to the Chat website. 
  2. Enter all your information. 
  3. Hit Submit when you're ready. 


Afterward, they'll be in touch with you as soon as possible. 


Let me know how it goes. I want to make sure all of your concerns are addressed. I'm only a few clicks away if you need me. Take care!

Level 1

Auto Payroll

Is there a cost?


QuickBooks Team

Auto Payroll

Thanks for joining on this thread, @aleggett.


I'm happy to tell you that communicating with our Customer Care Team is included in your QuickBooks Online Plan. That being said, there's no cost to reach them. 


See the screenshots below for the free features that you can use on your plan. 


qbo features 3.PNG


You may refer to this article: QuickBooks Features.


Ensure to call them within business hours to guarantee we can cater to your concern promptly. 


I've also added an article that might help in handling your QBO account such as your payroll, banks, etc.: Help Articles.


Feel free to let me know if you have other questions about your account. I'm willing to help you out. Keep safe. 

Level 1

Auto Payroll

How does quickbooks show or tell me how much state, fed, ssi, etc. taxes to take out of my one employees check? I have business checks with the paystubs attached to them, i am new to all of this and would like some help?

QuickBooks Team

Auto Payroll

I'd be happy to share some details about managing your payroll, @Mttom.


The payroll taxes that will be withheld from the employees' paycheck will vary on the four factors according to the Internal Revenue Service:


  1. Gross Pay
  2. Pay Frequency
  3. Marital Status
  4. Number of Allowances

To ensure that you've got the correct amount of taxes withheld from your employees make sure that you've filled out their details in the Employees page when adding each employee. Here's how to add your employee:


  1. Go to the Payroll menu and select Employees.
  2. Select Add Employee button.
  3. Enter the details needed and click Done.

Also, to know the updated wage base and the calculations of the payroll taxes, I'd recommend reading the IRS Publication 15 Circular E 2021. Speaking with your accountant if you have free time will also help you learn more workarounds about payroll and making sure that your books are accurate.


I've included articles that can show you how QuickBooks calculates Payroll taxes: 


You're always welcome to tag my name below if you have other concerns or questions. It will be my pleasure to share some insights.

Level 1

Auto Payroll

How does quickbooks show or tell me how much state, fed, ssi, etc. taxes to take out of my one employees check? I have business checks with the paystubs attached to them, i am new to all of this and would like some help?

Level 1

Auto Payroll

I have used auto payroll for the last 6 months, and love it. However, out of the blue, this week I received a notification that it has been turned off because of "some changes to my account" - which I haven't made any changes to my account. I meet all of the criteria listed in this thread, but QB still states that I'm ineligible. I need help understanding what the issue is so I can correct it.

QuickBooks Team

Auto Payroll

Thanks for reaching out in the QuickBooks Community, @TBronson.


Since you're still unable to use Auto Payroll after meeting all of its criteria, I'd recommend reaching out to our customer support. This way, they can review your account and check what's causing the ineligibility prompt.


Here's how you can reach out to them:


  1. Click the Help menu in the upper-right hand corner and click Talk to a human.
  2. Type in "Talk to a human", then press Enter.
  3. Look for I still need a human and click on it.
  4. Select Get help from a human.
  5. Choose between Chat with usSchedule an appointment, or Have us call you.

contact qbo support.PNG

Please check out our support hours to ensure that we address your concerns on time.


In case you have employees who aren't enrolled in Auto Payroll, you can run any regular payroll and print your paychecks if needed.


Don't hesitate to tag my name in the comment section below if you have other concerns or questions. I'm always ready to help.

Level 1

Auto Payroll

Help me now my employees will leave because this program keeps messing with their pay !!! The auto payroll just stopped for no reason!!!!!!! Today is pay day!!!!!!  call me now [phone# removed] Ms Bryan

QuickBooks Team

Auto Payroll

Hi Myralyn,


I know how important payroll is to your business especially to the employees I can relate coz I'm an employee myself. Let me have you contact our Chat or Phone support instead since we're unable to make phone calls in the Community. They will be able to get your account information in a more secure environment and check your payroll.

  1. Go to Help (?) and click the Search tab.
  2. Select Contact Us.
  3. Enter your concern in the box, say payroll issue, then select Let's talk.
  4. Choose a way to connect with us:
    • Start a chat with a support expert.
    • Get a callback from the next available expert.

If you have other concerns, feel free to go back to this thread.

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