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Accept Card Payments with PayPal app FAQ

Get answers to frequently asked questions about setting up the Accept Card Payments with PayPal app in your QuickBooks Online.

Note: To download, visit our App Store or select the Apps tab in QuickBooks Online.

What are the benefits of the PayPal app?

The Paypal app provides four key benefits:

  1. Low credit card and debit card fees starting from 1.7% + 0.20 per transaction
  2. Easy to set-up or upgrade from the existing PayPal app
  3. Improved and simple checkout experience for your customers
  4. With debit, credit card and PayPal wallet, there are more ways to pay for your customer

Will this integration work with other third-party PayPal-QuickBooks integration software?

With Accept Card Payments with PayPal, there is no need to use another similar integration software. If you choose to connect another PayPal to QuickBooks integration software on top of this app, be aware that duplicate transactions may appear in QuickBooks.

How do I configure my PayPal integration settings?

To get to PayPal Settings:

  1. Select Apps from the left menu (only viewable by admin users).
  2. Select the My Apps tab on the top of the screen.
  3. Find Accept Card Payments with PayPal, then under the Action button, select  Settings.

What does each setting mean?

  • Automation - Choose if you want to bring in transactions made on PayPal (but not through QuickBooks), such as Expenses and Money In. This is the transaction sync functionality that was present in the previous Accept Payments with PayPal app.
  • PayPal account - All PayPal payment transactions (minus fees) will be assigned to this Chart of Account.
  • Defaults for income - Select an income account from the drop-down menu for PayPal income transactions to default to. You can also select the default GST code and choose if you want to use the name “PayPal Customer” or create a new customer whenever the integration does not recognise a customer.
  • Defaults for expenses - Select the default GST code for expense transactions brought in from the integration.
  • PayPal Fees - Select a pre-existing expense account for recording your fees on transactions from PayPal.
  • Import past transactions - Select a date range within the last 18 months and we will create transactions in QuickBooks to reflect the sales and expenses from PayPal during that time period.

How secure is the setup process?

We use the highly secure OAuth2 transfer protocol to transfer your PayPal information to QuickBooks Online.

What happens to my transactions after I change mapping settings?

All transactions will follow the new mapping setting, while the previous imported transactions will remain in their appropriate accounts.

Do I need to create invoices in PayPal and in QuickBooks Online?

You can directly create an invoice in QuickBooks Online and email them to your customers. This allows your customer to pay with credit card, debit card or PayPal wallet. When they make a payment to the invoice, payment is automatically created in QuickBooks Online and linked to the invoice.

What if I have a QuickBooks Online account, but don’t have a PayPal account yet?

If you don’t have a PayPal Business account, create one here.

What if I already have a QuickBooks Online and a PayPal Business account?

Great, set up will take just a few simple steps. Simply add the Accept Card Payments with PayPal app to your QuickBooks Online account.

Follow these steps to set-up:

  1. Click on the + New button and select Invoice
  2. Click on Connect to PayPal next to the payment options tick box
  3. Grant permission to connect your PayPal account
  4. Click on Launch PayPal which will direct you to the PayPal login screen
  5. Login and enter your password
  6. Follow the PayPal prompts 
  7. Click on Go back to QuickBooks Online
  8. Review account names set-up and category for fees
  9. PayPal is now connected to your QuickBooks Online invoice payment options 

You’ll then be able to use PayPal to receive payments in QuickBooks Online.

How does the Accept Card Payments with PayPal app work?

Connecting the Accept Card Payments with PayPal app is quick, easy and secure. The app will allow you to send invoices with a ‘Pay now’ button, so your customers can make online payments using Visa, MasterCard, American Express or their PayPal Wallet.

You’ll receive payments in your PayPal account and the accounting will be done in QuickBooks Online.

Are all credit card types accepted?

Yes, the most common credit cards are supported: VISA, Mastercard and AMEX.

Will the Accept Card Payments with PayPal app help save time entering PayPal transactions?

Yes. When a payment is received by PayPal, it will automatically sync with QuickBooks Online, and record detailed information including items sold, quantity, discount, taxes and so on. 

PayPal fees are also imported as an expense in your QuickBooks account. 

How much does the Accept Card Payments with PayPal app cost?

The app is free to download and use. You will need an Australian QuickBooks Online account and an Australian PayPal business account to use the app. 

PayPal merchant transaction fees apply for receiving online payments.

Learn more about PayPal fees.

Does the Accept Card Payments with PayPal have data import or sync functionality?

Yes, you can import up to 18 months of past PayPal transactions into QuickBooks through the PayPal Settings. There is also a real-time sync feature which will bring in all your transactions from PayPal into QuickBooks Online with support for multi-currency. 

What is the difference between PayPal automation and connecting PayPal as a bank account?

Here is a table of the differences in the transaction detail of the PayPal app automation and bank connection.

PayPal AutomationBank Connection integration
Transactions ImportedAll types*All types
PaymentsE-invoicing solutionN/A
Sales transactionsImported (detailed categorisation)Imported (only summary)
TransfersNot yet available (Coming Soon)Imported (detailed categorisation)
ExpensesImported (default categorisation)Imported (detailed categorisation)
User’s primary benefitDetailed sales transactions, helps with accounting, online invoice payments capability, multicurrencyCategorised expenses and transfers
User’s primary limitationUser has to manually categorise Supplier paymentsUsers do not get detailed sales transactions


Note: The sync feature will automatically validate and stop the transaction sync if the same chart of accounts is used for both PayPal sync and bank feed.

If my customer used a credit card to pay my invoice, what would I be charged?

If your customer paid with a credit card linked to their PayPal account, then the standard PayPal wallet transaction fees (domestic and international) apply.   

If your customer pays directly with their credit or debit card (not linked to a PayPal account), then the low card transaction fees apply, currently 1.7% + AUD 0.20.


PayPal account transaction fees (domestic and international) apply to all PayPal wallet payments which include linked bank accounts, credit and debit cards and PayPal balance.

The PayPal service is provided by PayPal Australia Pty Limited (ABN 93 111 195 389) which holds Australian Financial Services Licence number 304962. Please read and consider the Combined Financial Services Guide and Product Disclosure Statement before acquiring or using the service.

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