Showing results for 
Search instead for 
Did you mean: 
Level 1

merchant service account

I have two merchant service account numbers connected to my email.  I can see both accounts and switch between them when I log in to the merchant center via a browser.  However, in QB Desktop, I can only see the old one.  How can I get QB Desktop to see the new one?

5 Comments 5
QuickBooks Team

merchant service account

Hi there, @Blueheron


Thank you for choosing QuickBooks as your accounting tools. In QuickBooks, you can only use one QuickBooks Payments account for one company file at a time in QuickBooks Desktop.

Follow these steps to connect your payments account to a different company file.


First, Connect your payment account:  


  1. In QuickBooks Desktop, go to the Customers menu.
  2. Select Link Payment Service to Company File. If you see a message about credit card protection, fill out the fields and select OK.
  3. Enter the user ID and password you used to sign up for QuickBooks Payments. Then select Sign In.
  4. Press Connect. Or if you're transferring your payments account to another company file, tap Transfer and then Yes, transfer


After you connect your account, you'll see an icon on the homepage. This tells you you're signed in and connected to QuickBooks Payments. 


Second, Change the account QuickBooks puts money into. You can keep using the same account you've always used to deposit customer payments. If you need to, here's how to change the account


Lastly, Turn on payment options and online invoices. Now your accounts are connected. Here's how to turn on payment options and process payments.  


Let me know what you find after trying out the steps. I'll be right here if you need anything else. Have a wonderful day!

Level 1

merchant service account

I'm sorry, but I believe you have not answered my question.  I do have Quickbooks connected to my merchant service account, and I do not want to change the external bank account that Quickbooks puts money into.  My problem is that there are two different merchant service account numbers associated with my email login, an old one and a new one.  When I log in at, i.e., not from within Quickbooks, I can see both accounts and switch between them.  When I log in from within Quickbooks, I can only see the old one.  I want to only see the new one.  How do I make that happen?

QuickBooks Team

merchant service account

Thanks for the clarification, @Blueheron.


You'll want to unlink the old account first in your QuickBooks Desktop (QBDT) program and link the new one. This way, it'll only show the new account. Ensure there are no invoice link to the payment account before disconnecting it. Let me guide you how to do it your QBDT software.


Here's how:

  1. Go to the Edit menu and select Preferences.
  2. Select Payments and then click the Company Preferences tab.
  3. From the Online Payments section, uncheck the payments method and select OK to save the changes. 2.PNG
  4. Then click Apply to existing customers.

You can also go to the Customers menu and select Unlink Payment Service to Company File.


Once done, link your new payment account to your QBDT. You can read the Connect your payments account section in this article for the detailed steps: Connect your QuickBooks Payments account to QuickBooks Desktop.

In addition this, I'm adding this great resource that provides complete information on how to personalize your invoice: Use and customize form templates.

You can always get back to me whenever you have other concerns. I'll be around to help you anytime. Keep safe!

Level 1

merchant service account

That did not work.  

I have noticed that while I cannot see any credit card deposits from the new merchant account using the "Merchant Service Deposits" button on the home screen, I can see them using the "Record deposits" button.


QuickBooks Team

merchant service account

Thank you for getting back to us, @Blueheron


Since the troubleshooting steps provided by my colleague didn’t work, I suggest reaching out to our Payments Support team. 


They can check your account in a secure environment and further check what causes this inconsistency. 


You can go to the following article to get their phone number: Contact Payments Support.


Let me know if there’s anything that I can help with your account. I’m always here to help. Have a great rest of the day!

Sign in for the best experience
Ask questions, get answers, and join our large community of QuickBooks users.
Sign In / Sign Up

Need to get in touch?

Contact us