How do I record an invoice payment on Qbooks when it comes through Paypal and amount received is minus the paypal fee?

Happy to have you here on the Community page, @y_dunlop.

Let me share the detailed steps so you'll be to record the invoice payment and the fee accordingly.

First, you have to record a Receive Payment and deposit it to the Undeposited funds.

1. Select Receive payment under Customers from the +(New) icon.
2. On the Receive Payment page, select a customer name under the Customer section.
3. Look for the invoice you want to pay under the Outstanding Transactions section.
4. Enter the payment amount under the Amount received section and choose Undeposited Funds under Deposit to.
5. Save the transaction.

Once completed deposit the amount, then add the PayPal fee as a negative amount under the Add funds to this deposit section.

1. From the +(New) icon, select Bank deposit under Other.
2. Pick an account where you want to deposit the amount under the Account section.
3. Locate the payment under Select the payments included in this deposit section, then mark the box beside it.
4. Go to the Add funds to this deposit section, then select the account for the fee and enter a negative amount under the Amount column.
5. Click on the Save and close button to record the transaction.

Get back to me if you have any other questions. I'm always here to help. Have a good day!