Quickbooks Payroll on its own creates new checking account in Quickbooks when payroll is submitted

Thanks for reaching out to the Community forum, @David P2. I appreciate you providing detailed information about your concern.

Let's go to your payroll setting to review the accounts set up on your accounting preferences to ensure that your payroll is posted correctly on the General Ledger accounts.

Here's how:

1. Go to the Gear Icon at the top.
2. Select Payroll Settings.
3. Click Preferences.
4. Select Accounting Preferences.
5. In the Bank Account section, review the account setup and make sure to select the correct account.

For additional reference, you can check this article on how to set up Payroll account preferences. 

Once done, you can run a payroll report to check if the amounts are accurate in your QuickBooks Online (QBO) account. Also, I encourage checking our Employees and payroll taxes page for reference. From there, you can read some of our great articles and learn some tips in managing your payroll.

Let me know if you have any other questions. Simply click the Reply button below to add a post. Have a wonderful day. 

I checked (again) the Payroll Settings under the Settings (gear) option.  The "Export Transactions" preference is properly set to the correct account where the payroll expenses are SUPPOSED to be recorded.  However, Quickbooks Online Payroll does not record the expenses there.  It creates the "Business Checking" account on its own and records them there.  We have deleted this non-existent Business Checking account several times and each time we do payroll again, QB Online Payroll recreates the Business Checking account.  Your instructions did NOT resolve the problem.

I wish I could make it better, @David P2.

The created checking account is how QuickBooks attempts to track your payroll expenses in one account history. This account can be found on the Checking Account section of your Accounting Preferences from the Payroll Settings menu.

Since you've mentioned the account has been set up correctly, yet it's still creating a new one, I'd recommend contacting our Customer Care Support. Even if you've already reached out to our team, only our specialist online has the tool to pull up your account information.

By doing so, a ticket will be created letting our engineering team investigate why this is happening saying it started last August this year. You can do so by following the steps below:

1. Go to Help.
2. Select Search.
3. Click Contact Us.
4. Enter a few words describing how the checking account is created after submitting your payroll.
5. Select Continue.
6. Click Chat with us or Have us call you.

You may also read this reference that'll allow you to manage security settings and keep your payroll account information up-to-date: Help Articles for QuickBooks Online Payroll.

If there's anything else that I can help you with aside from updating your payroll settings, please let me know in the comments below. I'll be here to lend a helping hand. Take care and stay safe!

This EXACT same issue is happening to a client of mine, QuickBooks has continuously told me they do not know why. Each time my client runs their payroll I just have to "merge" the two accounts which is better than making a whole JE to fix it, but if settings are set for the correct bank account then why doesn't it work without us having to merge them each time? Flaw of QuickBooks! And zero help from customer service, making both us and QuickBooks look very unprofessional. 

Hello kmeshe1220! Thanks for joining this post.

I'll feel the same if I'll encountered this too. Good to hear that you're able to merge the accounts.

I suggest you reach out to our Support Team again so they can create a case about this so that our engineers can investigate the cause of this behavior.

1. Click the (?) Help icon and enter Talk to a human (then type it again when prompted).
2. When asked by the bot, enter "Accounting Preferences".
3. Select I still need a human, then proceed with Contact us or Get help from a human.
4. Choose either Chat or Callback.

I also included these links if you want to connect your bank account to easily download the bank transactions:

• Connect bank and credit card accounts to QuickBooks Online

• Categorize and match online bank transactions in QuickBooks Online

I'll be here if you need more help with payroll. Take care!

Yes, sadly I have reached out to QB's professionals for my client 3 times now. Was just now finally told that it is a QuickBooks outage Investigation number 61604. My question is how long will this outage be? From the looks of this original post it has been happening since June. It is nice that merging is a quick fix, but the fact that my client has to call and get help fixing it each week sometimes twice a week is not an answer. Hoping that QB fixes this soon, as it can result in loss of software customers. 

We just ran payroll again and the same thing happened again.  This is utterly absurd.  We have submitted complaints through the "Feedback" option at least four times and talked to customer service more than a dozen times about this problem.  IT IS NOT SOLVED.  We have repeated the problem with representatives ad nauseum.  If there actually is a supposed "investigation" going on, then what is the status of it? 

The Contractors interface is different from employees.  The Contractors interface allows the user to select the bank account from which the money will be paid and it works properly by recording the payments to the proper account. 

I do not understand why Employees payroll would not be set up the same way.  Simply let the user select the payment account.  Instead, QB Payroll Online creates a brand new, nonexistent "Business Checking" account.  STILL NOT RESOLVED AND EXTREMELY AGGRAVATING.  I ABSOLUTELY WOULD NOT RECOMMEND QUICKBOOKS PAYROLL TO ANYONE.  End of year is coming and that's a great time to drop it.

I have been dealing with the same since June. I reached out to QBO help desk/support, whatever you want to call them, and got nowhere after countless hours spent trying this and that and talking to supervisors and the supervisors supervisors, the super users, the tech experts, subject matter experts, and every genius at QB and nothing. Utter useless.

Well QB really done it now. This month has been a nightmare. First the 1099NEC update screwing up all my vendor 1099’s. Now this whole month mysteriously created its own company checking account for all payroll and tax payments. Think it’s time for a new accounting software. I will not lose money sitting on the phone with these people. I’d rather waste my time setting up a new account with another company. After 15 yrs unreal. Please don’t respond with the same old how to set up an account for payroll. As that’s been correct for years!!! You figure it out and fix it. 

I am now in the same boat. The first time that the payroll program just created this separate "business Checking account" was on Feb 15, 2022. I see that some people have had a problem with this all the way back to the middle of last year. When this happened two weeks ago, I contacted QB for help, first in a chat that got me nowhere and then in two phone calls which burned up my entire afternoon. The fix was to merge accounts and so now I run the payroll again today, Feb 28 and same thing happens. Like I said, this hadn't happened to me previously, in fact, the payroll program has always worked quite well. A google search and I find this message and thread and then see that this has been a problem for QB for maybe as long as 9 months. Good grief, fix it already

Case ID#[removed]

Investigation# 56670

We are continuing to experience a problem in which Quickbooks Online Payroll which we have had for nearly a year now.  WE HAVE GOTTEN NO ANSWER AT ALL FROM REPEATED INQUIRIES IN WRITING AND BY PHONE FROM QUICKBOOKS PAYROLL.  Each time that we run payroll, Quickbooks itself creates a “Business Checking” account and places the payroll amounts in the non-existent account.  The “Business Checking” account, of course, has a negative balance.  The payroll amounts are supposed to be automatically entered into our established operating account.  We have to move the amounts into the operating account by creating a journal entry.  This has been happening since at least August 2021.

We are new users to Quickbooks Online Payroll.  We are NOT happy with the service for which we are paying $124/month including Quickbooks and the payroll service.  This seems like a major programming flaw.  We wonder what other flaws and errors Quickbooks likely is creating, especially with payroll.  We are debating whether to drop this service entirely.

We have spoken with customer representatives and they say this is a known problem with numerous users that “engineering” is working on.  We want this problem fixed promptly and we want to know when that will happen.  Quickbooks also should not charge us for the service during months in which this has been a problem.

WILL THIS PROBLEM EVER BE RESOLVED?  WHAT IS THE STATUS?

We just migrated to QBO in May '22 and noticed we have two payroll accounts too... we were so confused! It appears this issue is not fixed a whole year later and still occurs for new clients. Has anyone figured out to make it right???

I did figure it out. I believe it’s when I use my payroll app on phone. To fix the issue you need to merge the the second account by going into chart of accounts then change the name so it’s the same as your original account for payroll. Once that’s all said and done the second account will go away then you can match your transactions. 

This happened to me a few times and once I stopped using the phone to quickly do payroll the issue stopped. 

One other thing you need to check. Go into your payroll settings and check if the account payroll is being paid from is the original account that you set it up on. If it is then your ok. 

This issue just happened to one of my clients this week. Customer Support is not only completely unhelpful but a huge waste of time. A quick search and its evident here that this is a QB issue! But customer support went so far as to suggest today that "there's no guarantee that Quickbooks made the error" and I must have changed something. It is completely unacceptable that this issue has been ongoing for so long and still not fixed.

This is just happened to me as well. New Checking account in my chart of accounts with a negative balance equaling this weeks payroll in it. The new account has the same account number as my actual account but with a - in front of the # preceding the last four of the account. First the chat supports asks if someone on our end did it, then said that Intuit does not have the ability to modify accounts, then we go through the audit log and see that "system administration" created the account in the early hours of the morning. So then the solution was to go into settings, change the payroll chart back to the correct account, and then create manual journal entries for each payroll, then deactivate the account. These are the type of experiences that really make looking for an alternative provider an attractive solution.