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Level 3

Invoice Paid by QuickBoooks Payments Conflicts with Bank Transaction

We have been providing the option for clients to pay invoices using QuickBooks Payments for a while, but it's rarely actually used. A client paid us using this method recently. When the payment was placed, QBO automatically marked the invoice as "paid." A day or two later, the deposit transaction from our linked checking account showed up in Transactions > For Review. While this would normally "match" quite easily to the outstanding invoice, the invoice was already marked as paid. Now I can either "exclude" the real transaction, or figure out how to undo the automated payment to properly match it. This seems like a pretty major oversight.


I would much rather NOT match the payment from QB Payments as that's not a real account, is inconsistent with our standard practice, and could easily lead to confusion in the future.


Is there a way to disable that automated action of closing out the payment? What is the appropriate way to deal with this issue?

3 Comments 3
QuickBooks Team

Invoice Paid by QuickBoooks Payments Conflicts with Bank Transaction

I’m delighted to have you here in the Community, @itsGreghere. I’ll help you with matching yours bank transactions in QuickBooks Online (QBO).


With QuickBooks Payments, customers have the option to pay their outstanding invoices at their own convenience. You can accept electronic payments such as credit cards and ACH transactions immediately from an invoice or email if you use QuickBooks Payments.


With this feature in it, once the customer pays their invoices, QuickBooks will automatically mark the invoice as paid.


To help you with your concern about matching the transaction from your bank to your QuickBooks Online we can create a bank deposit to add the amount of the invoice as well as the bank processing fee.


Let me show you how:


  1. Select + New.
  2. Under Other, select Bank deposit.
  3. From the Account ▼dropdown, choose the account where you want to put the money into.
  4. Add the transactions under Add funds to this deposit.
  5. Under Received From, select the customer who paid the invoice.
  6. Add the necessary details, and ensure to input the correct Amount of the transaction.
  7. Add another line item to enter the amount of your bank processing fee, and ensure to input the correct Amount.
  8. Select Save and new or Save and close.



Once done, you can now match this transaction with your bank transaction in QuickBooks Online.

I also highly recommend you consult your accountant for expert advice on what account to choose for this specific transaction. 

To learn more about recording and making bank deposits in QuickBooks Online, you can check that here.

Here are a few articles to help you make sure your accounts are accurate and matched.



Know that the Community is always here to assist you with your banking transaction concerns. Just hit me up if further assistance is needed. Keep safe!

Level 3

Invoice Paid by QuickBoooks Payments Conflicts with Bank Transaction

This response is incorrect and addresses a completely different situation than I explained above. Please remove it.


Invoice Paid by QuickBoooks Payments Conflicts with Bank Transaction

Hello @itsGreghere,


I appreciate you for getting back to us about the payment concern. Allow me to step in and provide information about the customer payment.


When using QuickBooks Merchant Services, payments are matched to invoices by the system.  Every customer payment appears in QuickBooks, so you no longer need to record them manually.


Currently, the option to disable the automated action of matching invoices is unavailable. The only workaround for users using bank feeds is to exclude the downloaded data.


For your additional reference, I've attached a link you can use if you no longer need the QuickBooks Payments subscription: Cancel your QuickBooks Payments subscription.


Reach out to me anytime you have further questions about the QuickBooks Payment features. The Community and I will be around to help you.

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