PayPal is one of the most popular online payment processors… and if you’re a WooCommerce store owner and you use QuickBooks Online, you can easily accept payments in WooCommerce AND seamlessly record them in QuickBooks!

Our WooCommerce Sync for QuickBooks Online integration has fantastic support for PayPal payments, and once configured correctly both in our settings and in QuickBooks Online – you can achieve seamless accounting for PayPal sales.

How to Sync PayPal Payments on WooCommerce to QuickBooks Online

Only a few steps required to be able to integrate WooCommerce and QuickBooks to sync your PayPal payments and achieve seamless accounting.

The most important step is connecting your PayPal account to your PayPal bank account in QuickBooks Online.

First, add your PayPal Account as a bank account in your Chart of Accounts in QuickBooks. Then visit your Banking tab in QuickBooks Online to connect your account.

When you first connect your PayPal bank account in QuickBooks Online to your PayPal account, you’ll be presented with a screen to connect your PayPal account and sign in – so that future PayPal activity shows in the Banking tab of your QuickBooks Online account – for you to Add, Match or Exclude.

Once you’ve connected your PayPal account to QuickBooks, you’ll see transactions showing up in the Banking Feed. When PayPal pulls in sales amounts, it will pull in two line items – the gross amount, and a negative amount for the transaction fee.

TIP: It’s super easy to add a Bank Rule to automatically record this negative amount for the transaction fee. This way you can easily match the gross amount line item to the sale we’ve synced into QuickBooks, and you’ll be all set!

Match WooCommerce and QuickBooks Online Payment Gateways

If you would like to take this integration one step further, you may use our WooCommerce Sync for QuickBooks Online to sync your WooCommerce PayPal payments to QuickBooks.

To do so, you will first need to select a plan with us here,  install the plugin in your WordPress site, and then follow the first set of steps to connect your store to QuickBooks and configure the sync, and then to map your initial data.

Once you have completed the above, you will be able to map PayPal the corresponding QuickBooks Online payment method.

Here’s how you do it:

1. Visit MyWorks Sync > Map > Payment Methods.

On this page you will see each payment gateway you have enabled in WooCommerce. There’s one section for each WooCommerce payment gateway you have activated.

2. Enable payment syncing for PayPal

3. Select the corresponding QuickBooks Online Payment method

4. Select your QuickBooks Online “PayPal” bank account

Doing this will ensure that we’re correctly syncing PayPal payments from WooCommerce to be deposited in the correct QuickBooks bank account.

And that’s it! Once set up, you’ll be able to easily accept PayPal for orders, have payments automatically synced into QuickBooks with the transaction fees automatically recorded. Then just simply click Match in your Banking feed to make reconciliation a breeze!