Hi there, lkoups.
Thank you for providing detailed information with your concern so I can share accurate details and solutions. I'll provide information first on how PayPal fees are handled within QuickBooks Online.
For sales, fee amounts are obtained from PayPal and will be added when you match or add a transaction. They are not shown as separate transactions in the feed and will be recorded as an expense in your PayPal account. For one-off fees or fees not associated with processing a transaction, these usually come across as a separate expense in your feed.
To manage the situation, I'd suggest to manually received payment in QuickBooks and record the invoice payment in full. Then, make a deposit and add the bank fee as a negative amount.
Here's how:
- Go to the Plus icon and choose Received payment.
- Select the name of the customer from the drop-down menu.
- From the Outstanding Transactions section, select the transactions that you’d like for QuickBooks Online to calculate. As you select these items, the payment total will change.
- Select the Payment Date and the Payment method.
- Select Undeposited Funds in the Deposit to field.
- Fill in the other nessesary field.
- Click Save and close.
For additional information, you can click this article: Record invoice payments in QuickBooks Online.
Once done, you can now follow the steps below on how to go to the Bank deposit screen to start making a deposit to add a bank fee.
- Click the + New button and select Bank deposit.
- Select the bank account in the Account field and enter the Date.
- Under the Select the payments included in this deposit section, mark the invoice payment.
- Go to the Add funds to this deposit section and select the bank fee account in the ACCOUNT column.
- Enter the bank fee as a negative amount and hit Save and new.
Once done, the total amount should be the same as the one that reflected on your actual bank account and you can now match transactions. Please refer to this article to see the process: Categorise and match online bank transactions in QuickBooks Online.
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!
