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Everything you need to know about banking in QuickBooks Online - Discover more
Writem Limited
Level 1

PayPal Fees

I took a QB subscription a couple of months after our business started trading and we therefore had existing transactions in our bank account - all services paid for by customers via PayPal. The transactions QB sees in my accounts are the receivables from the bank - the cost less the PP fee - not the full invoice amount. How do I update these transactions in QB to reflect the full invoice amount and then the PP fee? 

QuickBooks Team

PayPal Fees

I see you want to update transactions in QuickBooks Online to show the full invoice amount and the PayPal fees, Writem.


Let me share some insights about it and walk you through the steps to rule this out.


If you use a third-party merchant service to take credit card payments from customers, the credit card company will deduct bank service fees from the payment. As a result, the deposit amount in QuickBooks Online won't match the payment amount that appears on the bank register.


You can manually record the transactions using the information from your bank statement. This way, the entire amount will appear and you're able to account for the fee at the same time. I'll show you how:


  1. Click on + New.
  2. Choose Receive Payments, then type in all the payment information.
  3. Tick the checkbox next to the invoice you want the payment to be applied to.
  4. Hit Undeposited funds as the deposit to account.
  5. Select Save and close to record the transaction.
  6. Click on + New.
  7. Choose Bank Deposits. You should see the payment you entered in the Select Existing Payments field at the top.
  8. Put a checkmark to select the payment you want to deposit.
  9. Go to the Add other funds to this deposit section, and fill in the amount of the PayPal fee as a negative amount.
  10. Go to the Account section, choose the Expense account you usually use in tracking bank fees.
  11. Check that the deposit amount is correct.
  12. Click on Save and close to record the transaction.


After that, you can already match the transactions from the Banking page going forward.


Once you're good, browse this additional guide on how to keep your books in order: Reconcile an account in QuickBooks Online.


You can always comment if you need extra help with banking, invoices, or QuickBooks. I'm always ready to back you up. Keep safe.

Writem Limited
Level 1

PayPal Fees

Thanks, I tried this but when I selected the customer name I already have set up when filling in 'receive payment' I got a warning saying I don't have any open invoices and to use a sales receipt.


I only recently joined QB, I'd previously invoiced through my bank. The amount per transaction QB saw when I connected to my account is the net amount of this invoice less PP fees. E.g. £400 original invoice, received £350 and the subsequently imported transaction into QB is £350. So I never invoiced via QB, which is why I assume I'm getting the warning noted above.



QuickBooks Team

PayPal Fees

I appreciate you for coming back to the thread for adding extra details about your concern, Writem Limited. Allow me to assist you in sorting out the issue you've received and ensuring that those customers' transactions are properly recorded in QuickBooks Online.


Please know that the downloaded data in QuickBooks Online depends on the information shared by the financial institution. However, the transactions that will appear in the Banking section will only be the customer's payments and expenses.


Since you've mentioned that you've never invoiced via QBO, I suggest generating the entry in QuickBooks manually. QuickBooks will automatically detect any match transactions already entered in QuickBooks Online from downloaded bank data to avoid duplicate transactions. This ensures that your records are correct and that you prevent errors when it comes time to balance your finances.


Here's how:


  1. Click the + New button,  then choose Invoice.
  2. From the Customer dropdown, select a customer. Make sure all of their info is correct, especially their email address.
  3. Review the Invoice date. Then from the Terms ▼ dropdown, select the due date.
  4. From the Product/Service column, select a product or service. You can also select +Add new to create a new product or service right from the invoice.
  5. Enter a QuantityRate, and Amount if needed.
  6. Fill in the other necessary fields.
  7. Click Save and close.


Once done, you can now follow the steps shared above on how you can manually link a bank deposit to an invoice in QuickBooks Online, ensuring that your invoice is marked as paid and your sales entries remain accurate. Furthermore, you can also have the option to link a deposit to a sales receipt. 


Lastly, you may refer to this article to see details on how the Sales page gives you a great at-a-glance view of the status of your sales transactions, like open and paid invoices: View sales transactions.


I’ll be around to help if you need further assistance with managing your invoices and other customer transactions in QBO. Just add them to your reply below, Writem Limited. Keep safe always!

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