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For everything you need to know at EOFY, view our EOFY FAQs.

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 new PayPal app?

The new 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 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

How can I get the benefits of the new PayPal app?

If you don’t have an existing PayPal app installed you can enable the new Accept Card Payments with PayPal app in a few simple steps. If you are already using the existing PayPal app, you can upgrade now to start getting benefits.

Is there anything different from existing PayPal app other than lower fees?

At this stage, the new PayPal app mainly focuses on accepting invoice payments. Transactions sync between PayPal and QuickBooks Online is not yet available. Our team is working to build new sync functionality which will be available in future releases.

Important: You will lose transaction sync functionality if you upgrade to the new PayPal app.

What are the current limitations?

There is currently no PayPal app sync function (only for existing customers), this feature is coming soon.

Will this integration work with commonly available 3rd party PayPal/QuickBooks integration software?

We don't promote a 3rd party software to connect your PayPal account with QuickBooks Online. With the use of this integration, there is no need to use another software in conjunction. If you choose to do so regardless, we recommend that you either use this integration or existing software (but not both - to avoid duplicate transactions from appearing in QuickBooks Online).

How do I configure my PayPal integration settings?

“PayPal Settings” takes you to view/edit the accounts from PayPal that map to the appropriate accounts in QuickBooks Online. By default, we choose a smart mapping method of categories to pick how it maps PayPal accounts to QuickBooks Online. If you are an advanced user, you can modify these settings during setup.

You can also choose to change these settings by going into the Apps tab, then selecting My Apps, finding your PayPal app card, selecting Action, then Launch.

Can you explain what each of the mapping screen drop downs mean?

Here’s what each of the settings mean:

  • PayPal account - To change this setting, select the pencil icon and use the drop-down menu to pick an account option of your choice from your Chart of Accounts.
  • 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 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?

With Accept Card Payments with PayPal, 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, a 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 PayPal, Visa and MasterCard.

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

Are all credit card types accepted?

Currently only VISA and Mastercard are accepted as a debit or credit card payment.   However, your customers can still use an AMEX card linked to their PayPal account.

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 etc. 

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?

The Accept Card Payments with PayPal app simplifies your bookkeeping by providing a breakdown of PayPal transactions, including fees, GST, income and expense, within QuickBooks Online. 

It doesn’t yet have the data import or sync functionality.

If you have the current Accept Payments with PayPal app and use it primarily for the data import feature, we recommend that you continue using this app until this feature is ready in the new Accept Card Payments with PayPal app. 

However, in order to access the new low debit and card transaction fees, starting at 1.7% and 0.20 per transaction you need to upgrade to the new Accept Card Payments with PayPal app.  

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.


*Currently excludes AMEX as a direct credit card option.   However, your customers can still use an AMEX card linked to their PayPal wallet.

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

add our PayPal standard disclosure statement below. This should be added in all the footnote wherever PayPal is mentioned. 

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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