Skip to main content
All CollectionsWebgility DesktopFeatures & functionality
Shopify Payout Reconciliation in Webgility Desktop with QuickBooks Online Integration
Shopify Payout Reconciliation in Webgility Desktop with QuickBooks Online Integration

Learn how to set up and use the Shopify Payout Reconciliation feature with QuickBooks online integration.

Virendra avatar
Written by Virendra
Updated this week

Overview :

The Shopify Payouts Reconciliation feature allows Webgility Desktop users to simplify the Shopify Payout reconciliation process with QuickBooks Online

You post your Shopify orders as Unpaid Invoices. When the payout is downloaded, a deposit for the total is placed. The orders that appear as paid in the payout will also be marked as paid in QuickBooks Online. This allows you to find outstanding orders that have not yet received a payment from Shopify.

To use this feature, you must meet the following requirements:

  • Be a user of QuickBooks Online.

  • Have payment processor fees and payout adjustments configured.

  • Ensure that orders posted into QuickBooks are marked as paid invoices.

  • Confirm the option Do not download refund is not selected.

  • Ensure the option to post refund settings is set up correctly.

Setup Instructions:

1. Configure the Posting Rules and Credit Memo Settings.

A. Configure the Posting Rules settings to record Orders.

Navigate to Integrations, Accounting POS/ERP, Posting Settings, and Orders.


Ensure the transaction type is set to Invoice inside the Posting Rule tab.


After selecting the Invoice, click on the Setup option.

In the Setup option, the transaction posting settings need to be configured.

  • Select the Terms, Terms Type, and Transaction Class options.

  • Enable the checkbox for Mark Invoice Paid.

  • Choose a Deposit to Account to record the payment of the order.

Enable the checkboxes for options such as Create Payment when posting payouts with the payment date as the payout date, Credit Memo, and Automated Refund Posting.


B. Configure the Credit Memo settings

After configuring the Posting Rule for orders, go to the Credit Memo tab at the top.

Select the Class and Terms options from the dropdown menu, then check the box for the option Create Refund Payment when Payout posted with payment date as the payout date, and select the Account Receivable account from the dropdown menu.


C. Configure the Auto Refund Posting settings

You must choose the Create Credit Memo option here. Once you have selected it, click Save and Continue at the bottom to proceed.

2. Configure Expenses & Fees to post the Payouts.

Make sure both the payment processor fees and payout adjustments are fully configured. This allows you to download and post your Shopify Payouts.

Navigate to Integrations, Accounting POS/ERP, Posting Settings, and Expenses & Fees

Inside the Payment Fees tab, Enable all the checkboxes to the options Record Payment Fees, Refund Recorded Payment Fees, and Download Payouts.

Next, choose the options from the dropdown menus to determine how expenses and fees will be recorded. The recommended settings are:

A. Record Payment Fee as Expenses.

Make sure to record Shopify payment processor fees as Expenses. You should use the same account you deposit payments into so it can make the invoice paid. Select Setup to configure the option.

In the example below, under the Expenses details, the account is Shopify Clearing and the Payment Date is the Payout Date. Fill in the remaining details according to your requirements.

B. Refund Recorded Payment Fees as Credit Memo

We recommend recording the refunded fees as a credit memo. Select Credit Memo from the dropdown menu, and in the last column, choose a line item to record the fee.

C. Download Payouts as Expenses/Deposits

Inside the Download Payout setup, download the Shopify payout and record it as an Expense/Deposit. Use the same account that is used in depositing payments, to make the invoice paid.

In the below example under the Expense/Deposit details, the Account is Shopify Clearing and the Check date is the Payout Date. Use an Expense for the type of account in QuickBooks to record the fees.

Note: Shopify Payouts data includes all of the fees, revenue, and transactions related to orders. If fees have a positive amount, Webgility will create an expense transaction as these fees are an expense to the business. If fees have a negative amount, Webgility will treat it as income and create a bill credit/deposit.

3. Enable Partial Refund download:

In the instance that an item is damaged or unsellable, you only pay a refund to the customer.

Navigate to Integration, Stores, and Settings.

Enable the option Get refund and record in. Select an item to record the refund amount.



Download Shopify Payout:

Navigate to Orders, Shopify, and Payouts to download the Shopify Payouts in Webgility.

When you click on the Shopify Payout page, it will show you all the downloaded payouts. If you don't see any, you can still download them.

Two ways to download payouts on Webgility:

  1. By Date Range.

  2. By Payout ID.

1. Download Shopify Payout by Date Range:

Navigate to Orders, Shopify, and Payout.

Click on the Get Payouts dropdown and select By Range to download the payout in Webgility.

You’ll see a popup window to select the date range from a specific date to download the Shopify Payouts.

2. Download Shopify Payout by Payout ID:

Click on the Get Payouts dropdown and select By ID to download the payout by Payout ID. To find the Payout ID, open that payout in Shopify and copy the ID from the URL.

Once the payout is successfully downloaded, it will appear and be listed under the Pending tab.


Post Shopify Payouts to QuickBooks:

You can post by selecting Payout and clicking Post to QuickBooks.

Once the posting pop-up is opened, it will check all missing and conflicting data, download missing data, resolve any conflicts, and post transactions in payouts.

Payouts will then move to Posted, and you can mark them as settled.

Now that this feature is set up, you can post your orders as you normally would. When downloading payouts and posting them to QuickBooks, paid orders will appear as paid on the invoice, and the deposit will show in the account register. The total will match the Shopify payout deposited in the bank.


Shopify Payout Detail View in Webgility:

To see details of the payout, you will need to click on the details view icon in that particular row.

In the detailed summary, you'll find the Shopify payout information, including total sales, refunds, adjustments, fees, and the deposit amount.

If you have any questions or need more help, please contact our support team.

Did this answer your question?