The business has recurring invoices set up to keep track of receivables. How do we have recurring payments applied to invoices or customer balances in general?

Good afternoon, @peds. 

It's great to see you back in the Community. I've got you covered. All you need to do is a few steps in your Merchant Services account to create those recurring payments. 

Don't worry. It's a simple process. Here's how: 

1. Sign in to the Merchant Services Center. 
2. Go to the Processing Tools menu.
3. Select Create a Recurring Payment. 

From there, you can choose the information needed for the payment. For future reference, here's a guide that will give you details about how to manage these recurring payments. 

These details should give you a better understanding of how you can create and manage these recurring payments. If you have any other questions or concerns, feel free to ask. I'll always be around to help out if you need me. Wishing you and your business continued success. 

That does not answer my question. I know how to setup recurring invoices and payments. Read the question more closely.

I can help apply the recurring payments into the invoices, @peds.

In QuickBooks Online (QBO), we can process recurring payments from your customers depending on the schedule you set using a sales receipt. I'll guide you how:

First, let's set up your recurring payments:

1. Go to the Gear icon.
2. Under Lists, choose Recurring transactions.
3. Click the New button.
4. Select Sales Receipt from the Transactions Type drop-down arrow.
5. Click OK.
6. Type in the name of the Recurring Transactions.
7. Choose Scheduled from the Type drop-down arrow.
8. Select the name of the customer drop-down and verify the email of the customer.
9. From the Payment Method drop-down, choose Credit Card Type.
   1. Enter your customer's credit card details.
   2. Click OK.
10. Select Save template.

Also, make sure to secure the written authorization from your customer before setting up their recurring transactions.

I've also added this article about how the customer pays invoices trough online: How to let customers pay their invoices online.

Don't hold your back to click the Reply button if you have other questions. I'm always willing to help you out. Take care!

That does not answer my question. Here is the question again:

The business has recurring invoices set up to keep track of receivables. We need a way to have recurring payments (using Quickbooks merchant services) to be applied to invoices or customer balances in general. Using a sales receipt does not work as it does not allow for the payment to be applied to “Accounts Receivable”. Furthermore, we can not get rid of the invoices as this will not allow us to keep track of A/R.

Your issue ends here, @peds.

At this time, the recurring invoices created in QuickBooks is not connected to the recurring payments you have in Merchant Services. That said, you'll have to manually apply the payments on the invoices instead. 

Also, you can consider following the steps provided by my colleague Maybelle_S above to set up recurring sales receipts in QuickBooks Online (QBO). I know that this process won't apply to the Accounts Receivable. However, this is the best way to manage recurring payments in QBO.

You might want to check out this article to learn more on how to manage recurring transactions in QBO: Create recurring transactions.

Please know that I'm just a reply away if you need any further assistance setting up recurring transactions. I'm always around if you need any help.