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How to connect PayPal to QuickBooks in 5 steps

connect PayPal to QuickBooks

With over 465 million users worldwide, PayPal is a must-have for ecommerce businesses. Supporting this payment platform can help online stores stay competitive by catering to a global market.

Manually entering PayPal transactions into QuickBooks is time-consuming. Unless you’re very careful, it can also lead to discrepancies which can cause errors with customer orders or taxes. That’s why it’s essential to connect PayPal to QuickBooks using an app.

In this blog, we’ll discuss how to set up the PayPal integration with QuickBooks including the step-by-step instructions, the requirements, and the best practices.

What you need to link PayPal to QuickBooks

Before you can connect PayPal and QuickBooks, set up the following:

  • A PayPal Business Account
  • QuickBooks Online or Desktop
  • A stable Internet connection


You’ll need administrator access to both platforms to log into the accounts and authorize all the changes.

How to connect PayPal to QuickBooks in 5 steps

Connecting PayPal to QuickBooks is relatively straightforward and takes less than an hour to set up. However, there are certain steps you should take to get the most optimal performance and avoid issues.

Step 1: Download the PayPal integration

If you haven’t already, log into your QuickBooks account. Go to ‘Apps’ and then ‘Find Apps’ in the menu. Search for ‘Connect to PayPal’ to find the integration.

QuickBooks Apps

Click on the title to open the QuickBooks app marketplace in a new window. Then locate the green ‘Get app now’ in the top left corner and click on that too.

Step 2: Sync your PayPal and QuickBooks accounts

QuickBooks will ask you to log into the PayPal account you wish to connect. Simply enter your credentials and follow the prompts.

Once you’ve connected, QuickBooks will automatically retrieve all your PayPal account details. It not only syncs your transactions but also any fees, withdrawals, and deposits.

Step 3: Review and select transactions

Before QuickBooks sync transactions to your account, it lets you check them. Uncheck all the boxes you don’t want to add to your books.

PayPal to QuickBooks

QuickBooks doesn’t sync temporary holds or releases by default. You have to enable these via the settings later.

You can select a data range for a historical sync. If you choose the wrong time frame, you need to disconnect your QuickBooks and PayPal accounts and set them up again.

Step 4. Check the PayPal app

Now you’ve connected the accounts, PayPal should appear in QuickBooks. Go to ‘Banking’ in the menu bar and you should see your balance. Don’t worry if the amount is incorrect — QuickBooks only syncs every three hours.

QuickBooks Deposits

Check your transactions to ensure they match. You can look at the time in the blue PayPal Bank box to see how long ago the platforms synced and whether they should be up to date.

Step 5. Configure settings

To customize your PayPal integration, go to ‘Transactions’ and then ‘Bank transactions’. You can edit all of the sections to decide which information to sync and what notifications you’d like to receive.

Tips for managing your PayPal QuickBooks sync

To get the most of PayPal for your online store, follow these best practices:

  • Make sure you have the latest versions: Both QuickBooks and PayPal update their apps continuously. By refreshing your software regularly, you can be sure your accounts have all the latest integration features.
  • Frequently reconcile accounts: QuickBooks has a reconciliation feature to help you match transactions. You can compare accounts, go through a checklist, and spot discrepancies. It’s best to reconcile accounts at least once per month.
  • Manage access and permissions: If you manage a team, make sure only experienced and trusted individuals can log into either PayPal or QuickBooks. You’re less likely to encounter errors due to mistakes or tampering.
  • Connect all your accounts: You don’t have to stop at linking PayPal and QuickBooks. Syncing ecommerce and accounting with an app like MyWorks means your sales and inventory data is always automatically up-to-date across platforms. MyWorks’ deep customization options allow you to map and sync data between ecommerce and accounting in the way that suits your business best.

Make the most of all your ecommerce and accounting apps

Ecommerce businesses can now benefit from a range of different payment options, including PayPal. The challenge lies in connecting them to not just your online store but also your accounting platform.

Apps like Connect to PayPal guarantee you can see all your transaction details in QuickBooks for accurate and efficient bookkeeping.

Looking for a more comprehensive integration? MyWorks syncs all sales from Shopify and WooCommerce into Quickbooks, including ones made through PayPal. You can map all your transactions so there’s no risk of recording something twice.

Discover the best MyWorks plan for your business.


FAQs about connecting PayPal to QuickBooks

How much does PayPal charge for QuickBooks?

There are no extra charges for using the PayPal QuickBooks sync. However, if you use QuickBooks invoices, PayPal fees start at 1.7% + $0.20 per credit or debit card transaction.

Can I connect multiple PayPal accounts to QuickBooks?

Yes, you can add multiple PayPal accounts to QuickBooks. Go to ‘Transactions’ and then ‘Banking Transactions’ in the main dashboard. You’ll see the option to ‘Add account’ which you can then click on and follow the prompts.

Can I connect PayPal to QuickBooks Desktop?

Yes, you can connect PayPal to QuickBooks Desktop. Note that some versions of QuickBooks Desktop are being discontinued so you may need to upgrade to support the integration.


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