I appreciate the additional information, Chris.
I can see how challenging it can be to encounter such issues. I'm here to help and guide you to the right channel that can address your concerns on time.
Situations like this one need special handling and in-depth troubleshooting to pinpoint the cause of the issue. We always prioritize the security of our customers' data, so I suggest contacting our QuickBooks Payments Support Team.
They're going to review your account settings and sales transactions. Our specialists will provide a detailed explanation of why Autopay paid the total invoice amount even with a credit applied. Then, walk you through the process of applying a permanent fix once it's ready.
On the other hand, you can consider turning off the Automatically apply credits feature so you can decide which open invoices you want to apply credit memos to. Here's how:
- In your QBO company, head to the Gear icon ⚙ and choose Account and settings.
- Go to the Advanced tab and click the Pencil icon for Automation.
- In the Automatically apply credits section, move the slider to the left to disable the function.
- Click Save and Done.
You'll find in-depth information on when to issue a credit memo or delayed credit to customers, as well as instructions for removing auto-applied credits from invoices through this link: Create and apply credit memos or delayed credits in QuickBooks Online.
In the following resources, you'll get answers to frequently asked questions about AutoPay, ways to manage your recurring entries, and handle various payment-related activities:
Feel free to tag me in your reply for any additional questions about applying the credit memo to your invoices and other QuickBooks-related tasks. I'll get back to make sure everything is taken care of for you. Have a good one, Chris.
