How do i treat a paypal fee in QB when we have received payment for an invoice minus the fee amount?

Hi accounts145, 

Thanks for your post. 😊 The steps below cover how to record receiving a payment minus fees in QuickBooks: 

1) Raise the invoice for the full amount manually (Sales > Invoices > New invoice)

2) Select 'Receive payment' on the invoice - enter the payment details and receive the full amount to the 'Undeposited funds' account on the 'Deposit to' drop-down

3) Create a bank deposit (+ New  > Bank Deposit) - make sure the date is when the payment hit your account 

4) Tick the invoice payment listed under 'Select the payments included in this deposit'

5) Scroll to 'Add funds to this deposit' - Set the 'Amounts are' drop-down to 'No VAT'

6) On the first line, enter the expense account for fees under 'Account', and enter the fee amount as a minus figure 

7) Check the total bank deposit amount in the top-right matches the payment received then save & close.

You can now match this transaction to the payment on your banking screen. As you've already recorded the expense separately, I'd advise deleting this to avoid duplications and follow the steps above to record this. 👍