A customer paid for two invoices from different accounts (branches of same company). How do I apply a single payment to two invoices from different accounts?

I'm here to share with you some information about invoice payments, @tom11_2-strainoptics.

In QuickBooks Online, you can apply a single payment to two invoices but for a single account only. This is to organize the payments once you deposit them. 

Here's how:

1. Go to the + New button and then select Receive Payment.
2. From the Customer dropdown, choose the name of the customer.
3. From the Payment method dropdown, select the payment method.
4. Select the account from the Deposit to dropdown menu.
5. In the Outstanding Transactions section, select the checkbox for the invoice your recording payment for.
6. Once done, click Save and close.
   

For more details, feel free to check out this article: Record invoice payments in QuickBooks Online.

Once done, you can deposit the money at your bank. To record this in QuickBooks, consider checking out this reference: Make bank deposits.

If you have any other concerns, feel free to tag my name in the comment section, and I'll get back to you. Have a great week and stay safe.

Hi Rubielyn_J,

Thank you for taking the time to reply. I think we've had a bit of a miscommunication, by "account" I meant the customer account, ie the profile under which the company addresses, phone numbers, emails, invoices, estimates and payments are stored and filed. Of course when a single payment is made, it by definition goes into a single bank account, I do understand that much!

The situation is, we have customers with branches all over the world. Let's say we have a customer, XYZ Company, with branches in New York City and Los Angeles. These are input in our Quickbooks with different profiles/accounts, since they have different addresses, contacts, and often different shipping accounts. We recently provided services to both branches, and invoiced them separately, with the invoices stored in the separate branch profiles. XYZ Company then paid for the two invoices with a single payment to our bank account. Normally, if a customer pays for two invoices, the payment can be applied to both, if the invoices are stored/filed under the same company profile. Can a payment be applied to invoices that are stored/filed in separate company/branch profiles? Or do I need to record the payment as two separate payments in order to mark those invoices as paid? If so, is there somewhere I can make a note (to make clear this "payment" is only part of a payment) so this does not cause problems in accounting?

Thank you

(System does not seem to allow me to reply directly to your reply, Rubielyn_J, apologies)