I'm here to assist you with recording the tax withheld by your customer in QuickBooks Online (QBO).
You can delete the payment linked to the invoice first, so you can apply the credit note to your invoice payments. Here's how:
Go to the Invoicing menu, then click the Invoices tab.
Locate and open the paid invoice, and select the pencil icon.
Click the payment link below the Payment Status Paid in the upper right corner. Then, tap the date link of when the payment was applied.
On the Receive Payment page, click the More button at the bottom and select Delete.
Choose Yes to confirm.
After that, recreate the credit note to include it when applying it to receiving the invoice payment. Then, follow the Step 4 of this article to record the tax withheld seamlessly: How do I record tax withheld by my customer?
Don't hesitate to add a reply in the comment section if you have clarifications about recording tax withheld or other QuickBooks concerns. I'm always around to help you again. Enjoy your day!
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