QB Issue Resolution:

Yes, there’s a way to apply your customer’s overpayment to their invoice. I got the steps to guide you through it, and we’ll not use the automatic application of credits.

  1. Open the invoice and click on Receive Payment.
  2. On the Receive Payment screen, enter the overpayment amount in the PAYMENT field of the invoice. Please see screenshot 1.
  3. If there are other unapplied payment transactions in the Credits section, unselect them.
  4. Click Save and close.
  5. Open the partially paid invoice and email it.

That’s all you need to apply the overpayment. If I’d be your customer, I’d be happy seeing the credit to my invoice even if it’s a small amount.

Resolution for Issue 'Is there a way of applying customer credits to invoices before they are sent? I want to do this for specific invoices not automatically.' available: Yes (Solved).
Source: Intuit Community forum.

Is there a way of applying customer credits to invoices before they are sent? I want to do this for specific invoices not automatically.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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