Hi there, Samuel. I can help you find the root cause so you can apply the payment to the correct invoices.
QuickBooks Online (QBO) automatically applies any available customer credits to newly created invoices.
To resolve it, visit your customer's profile and review the transaction. Make sure the payment applies to the correct invoice. You can follow the steps below:
- Go to My Apps, then select Customer Hub.
- Click Customers.
- Locate the customer name and the entry you want to pay in full.
- Choose the payment option and apply the payment using the Receive Payments feature.

You can temporarily turn off the Automation feature to ensure it won't automatically apply as payments.
Here's how:
- Go to the Gear icon.
- Choose Account & Settings.
- Click on the Advanced tab, then find the Automation section and toggle it off.
- Save and Done After.

Please let us know if you have any questions as you try these steps. We'll be here to address them for you.