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Intuit
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Accept payments with Paypal app FAQ

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

Note: To download, visit our app store or select the apps tab in QuickBooks Online.

General questions

It's an integration with PayPal that enables online invoice payments and syncs your transactions from PayPal into QuickBooks Online. It also monitors your PayPal account for other sales transactions and appropriately handle your expense transactions.

PayPal imports your sales and expense transactions including your bank transfers (from/to PayPal).

When a sale is recorded in PayPal, it is synced over to QuickBooks Online as a sales receipt, with the detailed level information, like the item sold, the quantity, discount, shipping, tax, etc.
It imports all expenses into a default expense category known as “Uncategorised Expenses”. If you need to group your expenses with the same details, you can do it manually.

Know the difference in how the certain transactions are being handled between the PayPal app and bank connection centre in QuickBooks Online.

New PayPal app Bank Connection integration
Transactions Imported All types* All types
Payments E-invoicing solution N/A
Sales transactions Imported (detailed categorisation) Imported (only summary)
Transfers Not imported (the destination/origin bank that is receiving/sending the transfer from/to PayPal will show the transfer instead) Imported (detailed categorisation)
Expenses Imported (default categorisation) Imported (detailed categorisation)
User’s primary benefit Detailed sales transactions, helps with accounting, online invoice payments capability,multicurrency Categorised expenses and transfers
User’s primary limitation User has to manually categorise Supplier payments Users do not get detailed sales transactions

* Except PayPal Credit and cash transactions

We are working together towards a solution that will merge these solutions into one.

Note: You can only enable one integration at the moment. The PayPal app will automatically greyed out if you turn on the Bank connection centre integration.

Disconnect your old integration and verify that you setup your PayPal account to import detailed sales transaction to QuickBooks Online.

Sign in to your QuickBooks Online account, then under Bank Accounts, you should see the connected PayPal account.

User-added image

To disconnect your Banking centre connection to PayPal:

  1. Go to Banking, then choose the bank account that is linked to PayPal.
  2. Select Edit ✎ next to the bank account.
  3. Select the Disconnect this account on save checkbox.
  4. Select Save and close to disconnect the PayPal account linked as bank download.
  5. Select the sign up link provided to you in the mail, then follow the intructions to setup the PayPal app.

Your PayPal account linked as bank download is now disconnected.

If you choose to accept online payments, PayPal may charge transaction fees on the payments processed. Connecting to this app and data sync functionality is completely free.

The current limitations are:

  • You can only setup one PayPal account per QuickBooks account via the Paypal app.
  • If the same PayPal account is connected to 2 QuickBooks accounts, the first connection will drop.
At this stage, you can't setup multiple PayPal accounts to the same QuickBooks account.
No, if the same PayPal account is connected to 2 Quickbooks accounts, the first connection will drop.
We don't promote a 3rd party software to connect your PayPal account with QuickBooks Online. However, 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).

Settings and mapping

“App 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 My Apps, finding your PayPal app card, selecting Settings, then App Settings.

Here’s what each of the mapping screens in the drop down means:

  • PayPal account - It's created in QuickBooks under the selected value. To change this setting, use the drop-down menu and pick an account option of your choice from your Chart of Accounts.
  • Sales - All your sales or income transactions from PayPal will appear in QuickBooks under the selected item. To change this setting, use the drop-down menu and pick a pre-existing sales account from your chart of accounts.
  • PayPal fees - All your fees on transactions from PayPal will appear in QuickBooks under the selected item. To change this setting, use the drop-down menu and pick a pre-existing fees account.
  • Default GST for sales - All your GST on transactions from PayPal will appear in QuickBooks.
  • Default GST for expenses - GST on Capital or GST on non-capital
  • Payment method on transactions - All your transactions imported from PayPal will have the payment method as the selected item in this drop-down menu.
  • PayPal customer - All customer details or no details that you choose to pull. By default we will use the integration default of pulling “All details” for tracking your PayPal customer details in QuickBooks.

The drop down menu in mappings settings does not show sub-accounts, though it will display them. You can select the sub-account as your QuickBooks mapping account. For example, if you created a sub account known as “My PayPal Sales” under “All sales” in QuickBooks, it will show up as the following:

  • Accounts
  • All Sales
  • My PayPal Sales

Now, if you would like to map your PayPal Sales to “My PayPal Sales” account in QuickBooks, you should select the following account:

  • Accounts
  • All Sales
  • My PayPal Sales
Once set up, QuickBooks syncs with PayPal every 15 minutes and brings any new transactions. You'll get a daily integration summary of these imports unless you choose to turn it off.

Other questions

You should be able to review your transactions after they import by selecting the following tabs within QuickBooks Online:

  • Go to Sales, then All Sales for sales transactions.
  • Go to Expenses, then Expenses for expenses transactions.

Your PayPal transactions will be imported with “PayPal” as the payment method, PayPal as the source, and PayPal Bank (by default) as the account.

We use standard secure OAuth transfer protocol to transfer your PayPal information to QuickBooks Online.

You can connect multiple PayPal accounts to QuickBooks Online, however you won’t be able to get sales transaction details for subsequent accounts. If you need to set this flow, contact us.

Ongoing use - Importing transactions

To manually import transactions in bulk:

  1. Go to apps.com, then select My Apps.
  2. Select PayPal, then Settings.
  3. Select Manual Import.

By default, Accept Payments with PayPal only import transactions that occured after the app was connected. During setup, we provide an opportunity to manually set it up.

What you should do:

  1. Go to apps.com, then select My Apps.
  2. Select PayPal, then Settings.
  3. Select Manual Import.
You'll receive a daily email with the transactions imported over 24 hours. You can also check QuickBooks if the transactions are imported in sales, banking, and expenses.

Here are several sample scenarios:

  • Scenario 1: You have unchecked the setting to receive daily import notification.
    What you should do:
    1. Go to apps.com, then select My Apps.
    2. Select Manage my apps, and PayPal.
    3. Select Settings, then App Settings.
    4. Select the Subscribe to transaction import summary and error notification checkbox.
  • Scenario 2: You didn't changed the default past transaction settings and there are no new transactions to import from PayPal.
  • Scenario 3: There is an Error in the transactions, you can check the Error Log.
  • Scenario 4: There are no new transactions in PayPal to import.

If your case doesn't fall in these scenarios, contact us for additional help.

If there are no transactions to import from PayPal, the integration will continue to sync for new transactions every 15 minutes, as per regular sync frequency. If there are no new transactions, you will not receive a daily import summary.

To disconnect your Banking Centre connection to PayPal:

  1. Sign in to your QuickBooks account
  2. Go to Accounting, then choose the bank account that is linked to PayPal.
  3. Under Action, select the small ▼ drop-down next to the bank account.
  4. Select Edit, then select the Disconnect this account on save checkbox.
  5. Select Save and close to automatically start your app again.

Ongoing use - Modify settings

  1. Go to apps.com, then select My Apps.
  2. Select Manage my apps, then PayPal.
  3. Select Settings, and Import settings and logs.

Note: You can't change the map setting while the past transactions are importing.

Additional PayPal FAQs

To import the previous transaction:

  1. Go to apps.com, then select My Apps.
  2. Select Manage my apps, then PayPal.
  3. Select Settings.
Yes, you can manually import transactions in bulk after going into settings.
No, the bulk import dates will not overlap with each other. Unless you select the Overwrite previous transactions checkbox.
  1. Go to apps.com, then select My Apps.
  2. Select Manage my apps, then PayPal.
  3. Select Settings, and Import settings and logs.

Note: You can't change the map setting while the past or manual (bulk) transactions are importing.

All transactions will follow the new mapping setting. While the previous imported transactions will remain in their appropriate accounts.
  1. Go to apps.com, then select My Apps.
  2. Select Manage my apps, then PayPal.
  3. Select Settings, and Integration Options and logs.
  4. In App Settings section, clear the Subscribe to transaction import summary and error notifications checkbox.

Usage patterns & errors

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 cards, debit cards or PayPal balance.
  1. Go to apps.com, then select My Apps.
  2. Select Manage my apps, then PayPal.
  3. Select Settings, and Import settings and logs.
  4. In Error logs window, select View.
  1. Go to apps.com, then select My Apps.
  2. Select Manage my apps, then PayPal.
  3. Select Settings, and Import settings and logs.
  4. In Error logs window, select View.
  5. Select Details to see the description of the error, then fix it.
  6. Select Retry after fixing the error.
We are currently unaware of any PayPal import errors. We'll update this article with known errors and their solutions as we learn from them.
No, the current integration app does not provide the capability to review sales transactions before importing them.

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