Let me clear things out for you. We can add the Paypal fee as negative when we create as bank deposit and record it as expense to clear out your deduction fee. By doing so, make sure to select the sales receipt as Undeposited funds to link the deduction fee and it'll match according to the downloaded bank transaction.
Here's how:
Select the +New button and click the Bank deposit.
Choose the bank where the payment will be deposited to.
Check all applicable payments.
Under the Add funds to this deposit section, choose the PayPal fee expense account and enter the fee in negative.
From there, you can now match this transaction to the on your banking screen. As you've already recorded the expense.
Please refer to this article to see steps on how you can reconcile your accounts so they match your bank and credit card statements to avoid discrepancies: Reconcile an account in QuickBooks Online.
Please let me know how this goes. I'm always here to help you further. Take care!
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