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Visit this post for a list of recent banking issues in QuickBooks Online.
Level 2

Online Invoice Payments - Full Workflow?

New to the community, thanks in advance for any help you can offer.


Can anyone explain how the integrated online invoice payments (via PayPal) is meant to work in the QBO back-end?


  • A customer has just paid an invoice by clicking the link on the invoice.
  • I can see a Payment and Expense created within QBO.
  • The Banking is asking us to review the money (net) that's landed in our PayPal account. I cant see a way to match this to the payment and expense, if I click add will it not duplicate the income?


I understand the process with manual PayPal payments, Undeposited Funds etc. But this "automatic" method doesn't yet fully make sense to me.


Any help greatly appreciated.

QuickBooks Team

Online Invoice Payments - Full Workflow?

Welcome aboard to the Community, MagCAD.

Let me share some information on how QBO handles PayPal payments.

When you create an invoice in QBO and send it to your customers, they can pay with a credit card, debit card, or PayPal wallet. When they make a payment, it’s automatically created in QuickBooks and linked to the invoice.

The online program will match the downloaded payment (PayPal) with the one you already entered. This process prevents duplication of transactions.

We’ll have to exclude the expense to keep your records correct. This ensures you can match the payment to the invoice.


  1. Click the Banking menu from the navigation panel and choose Banking.
  2. Go to the Banking tab and select PayPal.
  3. In the For Review section, tick the box for the entry you wish to remove.
  4. Hit the Exclude menu to move the entry to the Excluded section.exclude.png

Here’s an article that provides more insights into this process: Exclude a bank transaction you downloaded into QuickBooks Online.

After performing these steps, you can now match the payment to the invoice. Check out this article for detailed instructions. From there, you'll learn how to review and classify downloaded entries: Categorise and match online bank transactions in QuickBooks Online.

You can bookmark the following link for additional resources. It contains answers to common questions about recording payments via PayPal: Accept Card Payments with PayPal app FAQ.

Feel free to visit the Community again if you have other concerns. I’ll get back to help and make sure you’re taken care of. Enjoy the rest of the week.

Level 2

Online Invoice Payments - Full Workflow?

Hi Rasa-LilaM,


Thanks for the reply, however your answer doesn't quite match with what i'm seeing in QBO.


  • The customer paid the invoice using the online payments link.
  • QBO has automatically created a payment and linked it to the invoice.
  • QBO has automatically created an expense for the correct PayPal fees.
  • QBO has pulled the banking transaction in from my PayPal account, but it has no linked this with anything. Currently it is asking me to add or match, but there's nothing for me to match it to.


Any help greatly appreciated.

QuickBooks Team

Online Invoice Payments - Full Workflow?

Thanks for your prompt reply, MagCAD.


To help manage your situation, you'll want to record the receive payment in QuickBooks Online. Then, make sure to deposit the payment in the Undeposited Funds account.


Once done, create a bank deposit and add the bank fee as a negative amount. The instructions are included in these articles:


Lastly, go back to the Banking page and check if you see a match on your PayPal transactions. Please feel free to check the articles shared by my colleague Rasa-LilaM.


We're always around if there's anything else you need. Just leave a reply below and we'll get back to you as soon as we can. Take care and stay safe!

Level 2

Online Invoice Payments - Full Workflow?

Hi RenjolynC,


Thanks for the reply.


I understand this process you're describing when I manually take a PayPal payment.


However the issue I'm facing here is when the payment is taken with the QBO and PayPal integrated online payment.


"Save hours on admin - PayPal payments and fees are automatically recorded and reconciled in QuickBooks."


Please can someone explain the correct process in the QBO backend when the payment is received with the Quickbooks integrated online payment?


Online Invoice Payments - Full Workflow?

You're welcome, @MagCAD. It's our pleasure to help. 


I'm here to share additional information when the payment is received in QuickBooks that is integrated with PayPal.


If the bank that is connected to your PayPal account is also connected to your QBO account, you can see duplicate transactions. 


When you receive payments from PayPal, you can view them from your For Review section. Then, please take note of the PayPal fees. Those will be recorded as an expense. You can categorize them to the right account from there. Here's the categorize and match online bank transactions in QuickBooks Online article for more information. 


Going back to the duplicate transactions, you can choose either you'll be excluding the transactions from the bank or PayPal. You can refer to the steps provided by Rasa-LilaM above. See this article for detailed guidance: Exclude a bank transaction you downloaded into QuickBooks Online.


Here are some video tutorials that can help you achieve basic tasks with QuickBooks Online: Video tutorials for QuickBooks Online


Let me know if you still have follow-up questions about your transactions. I'm always here ready to help. Take care and have a great rest of the day!

Level 2

Online Invoice Payments - Full Workflow?

Hi MaryJoyD,


No, that is still not it.


We seem to be going around in circles here. How can I get someone at Quickbooks to take a look at our account, so you can understand the scenario we have before answering?


Nothing to do with Bank Account.


  • We have our PayPal account syncing with QBO, so we see when the money arrives in our PayPal account.
  • The invoice has been paid using the Online Invoice Payment link.
  • A payment and expense all created automatically by Quickbooks under the PayPal account.
  • The amount in QBO matches the amount in our PayPal account.
  • But Quickbooks has the transaction pulled through from by the account sync under review, it has not been matched, and if we add/categorise it we will be duplicating income.
QuickBooks Team

Online Invoice Payments - Full Workflow?

Hello again, MagCAD.


I'm here to clarify and give more details about your concern. 


When you have the Accept Payments with PayPal app integrated in QuickBooks, transactions are recorded and categorised automatically to your books. This means that you don't need to manually add or match what was downloaded from the For review page if your PayPal account is connected to Open Banking. Doing so may cause duplicate transactions in QuickBooks. 


What you can do at the moment is follow the steps provided by my colleague Rasa-LilaM on how you can exclude the transactions. Excluding a transaction from the For review page doesn’t appear in any account registers or financial reports.


To learn more about the process, you can read this article: Accept Card Payments with PayPal app FAQ.


If you still want to reach out to our phone or chat support, you can follow the steps below. They can do a screen share session with you and review your setup. 


Here's how:


  1. Click the Help icon located in the upper right-hand corner.
  2. In the Help window, click the Contact Us button located at the bottom.
  3. Enter your question and click Let's talk.
  4. Choose either Start a chat or Call us.

If you have the new QuickBooks Assistant help update, you can follow these steps:


  1. In your QuickBooks Online account, go to the Help > Assistant.
  2. Type Talk to a human and click the Contact a human button.
  3. Select Live Chat / Call me back.

You're always welcome to leave a reply on this thread if there's anything else you need. We'll be around to help you out some more. Have a good day!

Fiat Lux - ASIA
Level 15

Online Invoice Payments - Full Workflow?


Explore the trial version of this app to compare how it reconciles your PayPal transactions to QBO.


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