Hi,
thanks for the reply but I don't think this solves the issue as I'm currently doing both of those processes which is the problem - its coming in through WIX as a paid invoice and then its also coming in through the bank as a deposit (Stripe payment). I need to know how to remove one of these processes so that I'm not double counting.
I've tried matching the bank, but because the invoice shows as already paid through WIX (ie closed), it does not then appear in the list of transactions in QB because it only seems to show open invoices.
Would it make sense for me to record the payment against a WIX invoice as a sales receipt rather than a payment (is a sales receipt considered open?) so that then the only payment would be when the Stripe deposit is recorded. I would also then be able to match the transaction from the bank as it would appear on the open invoices list...? Or should I just exclude the bank deposits?
Thanks,
Yvonne.
Thanks for updating us about the payment receiving process in your company, @Garry.
Joining the thread to share some insights to resolve the receiving and matching problem in your account.
You can exclude the deposit if it is a duplicate of another bank transaction. Otherwise, if it needs to be included in the reconciliation, you can simply match the bank entry with the net payment in QuickBooks.
To do that, receive the payment with the fees in the Undeposited Funds account.
- On the invoice, click the Receive Payment button.
- Select the correct invoice on the Receive Payment screen.
- In the Deposit to field, choose Undeposited Funds.
- Click Save and close. (See screenshot attached)

Step 3: Enter a Bank Deposit for the fee to relieve the balance from Undeposited Funds account to bank account. (See screenshot)
- Click the QuickBooks Plus (+) icon.
- Select Bank Deposit.
- Mark the invoice payment you received previously from the Select the payments included in this deposit section.
- Expand the Add funds to this deposit section to add a new line item.
- In the Received From column, enter the vendor who charged the fees.
- In the Account column, add an expense account for the fee.
- In the Amount field, enter a negative fee amount.
- Make sure the deposit matches the net bank deposit amount.
- Click Save and close.

After depositing the funds in your bank, you should be able to match it to the transaction in the Banking page. See this link to learn more about matching bank transactions: Categorise and match online bank transactions in QuickBooks Online
If you need anything else, please let me know in the comment below. I'll be right here to help categorise your bank transactions. Have a good one!