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Hello there, @georgegaviria1.
Thank you for posting here in the Community. I can help you record the fee without showing it on the actual invoice.
You'll need to create a new service item and select an expense account.
After creating the item, create a credit memo and select the service you've created. Let me show you how.
Once done, you can check the transaction by running the Profit and Loss report.
Let us know if you have any other QuickBooks concerns. We're always here to help!