Of course I am talking about direct deposit for both accounts...

Let me share a few information, Karen.

Yes, you can use different bank accounts for each payroll subscription

I'll add some articles to help you set it up:

• Set up your company payroll for direct deposit
• Set up an employee for direct deposit

If you have other payroll questions, please don't hesitate to let us know. We're right here to help you. Keep safe!

I have the same issue here hoping to withdraw payroll from two different bank accounts under one company EIN(we have branches in different states).  Does QB desktop have solution now?

Hi there, @maytsaicpa.

At this time, QuickBooks can only withdraw payroll in one bank account under one company EIN.

I know that the option to withdraw payroll from two different bank account is beneficial for you and your business. For now, I encourage submitting feedback directly to our product engineers. They may look into this suggestion and consider adding the option in the future update. To send your feedback, you can go to the Help menu and select Send Feedback Online. Then, enter your product suggestion in the field and click Submit.

You can also visit our feedback forum to check the recent updates and added features in QuickBooks.

I'm still open to your replies if you have additional questions processing payroll in QuickBooks Desktop. Have a good one.

This post is three years old.  Has Intuit been able to fix this issue with direct deposit?

No, it's the same as it always has been.  I don't believe they have any intention to change it.  One bank account only for direct deposit regardless of how many bank accounts you have.

We have 1 EIN; 2 locations; and 2 bank accounts, one for each location. 

We want to run payroll for each location using the location's designated bank account. 

Payroll is via direct deposit,

Can we achieve this with one QB account?

Thank you!

Hello there! I appreciate you reaching out to us.

You can add and modify an employee's work location in QuickBooks Online Payroll to allocate wages to an area. I'd be glad to walk you through the process:

1. Login to your QuickBooks account credentials.
2. Click Employees from the Payroll menu.
3. Choose an employee.
4. Press Edit under Employment information.
5. Choose Add work location or modify the current from the Work location dropdown, then click Save.
6. Look up your address. Click Enter manually if your address isn't displayed.
7. Select Add Location after entering the address.

The hours, fees, or wages will be charged to the location when payroll is processed. You can also visit this article to learn about handling workers' locations: Set up and manage work locations in QuickBooks Online Payroll. 

Please be aware that it is not possible to split salary between locations. Our payroll services can currently only handle one local tax jurisdiction or SUI tax per employee.

I've also included this article that has details when the workplace changes: Set up employees and payroll taxes in a new state.

I'm grateful that you took the time to get in touch with us. Visit this thread if you have more inquiries location tracking. Have a nice day, 

rjtvp.

This seems like a workaround for assigning classes. 
However it does not address my and many other’s concerns about funding separate payrolls from separate bank accounts under the same EIN. 
plus, there is a lot of work needing to be fixed in QBO payroll. 

We're taking notes of your feedback and suggestion, @batgirl.

Currently, processing payroll with separate bank accounts is unavailable in QuickBooks. 

I understand that funding separate payrolls from different bank accounts is beneficial to you and your business. As an alternative, you can consider changing your payroll bank account every time you run payroll from a different location.

While this feature isn't available, I suggest submitting feedback directly to our product engineers. They may look into this suggestion further and consider adding the option in QuickBooks Online (QBO). To submit feedback, you can go to the Gear icon and select Feedback. Then, enter your suggestion and click Submit Feedback.

You can also visit our Customer Feedback page. This will help you track the status of your product request and get the latest updates from our developers. Updates such as how the recent enhancement made to QBO helps our business owners, like you.

Please touch base with me here for all of your QuickBooks needs. I'm always happy to help.

Thank you for your responses.

From the information shared, I am understanding that I have two options:

1. Pay for two separate QB accounts, one for each location, or

2. Have one QB account and change the bank account after running payroll for location 1 and before running for location 2, which is a length, involved process.

Am I understanding this correctly?

Thanks

Yes, you're right, @rjtvp. 

As funding from different bank accounts is unavailable in QuickBooks Online, you can consider creating another QuickBooks Online account with Payroll on a different location or using two different bank accounts for payroll if you don't use direct deposit.

On the other hand, you can also send feedback to our Product developers as stated by my colleagues above so this will be taken into consideration in future updates. You can refer to the steps indicated above or directly utilize this link so you can also get the latest updates from our development team: QuickBooks Online Customer Feedback. Just hit on the Give Feedback option and you can then enter your idea in helping us improve your overall QuickBooks experience.

I'm also adding this helpful article that'll help you get a closer look at your business' finances by running our available payroll reports: Run payroll reports in QuickBooks Online. You'll also get guidance on how to print and customize these reports. 

I appreciate you taking the time to interact with us in the Community forum, and as always, feel free to contact me with any additional payroll-related inquiries.  I'll be here to help you as soon as you click the Reply button. Have a great day.