Skip to content
  • There are no suggestions because the search field is empty.

Download and Post Shopify Payout Fees in Webgility Online

This article provides guidance to Webgility Online users on using the new feature in Webgility Online that allows to download Shopify payout fees and post them separately into QuickBooks Online. By separating fees from sales, businesses can maintain clearer financial records, simplify reconciliation, and improve expense tracking and reporting. The article outlines setup instructions, explains how the feature works, and highlights its availability for customers using Shopify with QuickBooks Online under the transactional accounting method.

Overview

Shopify deducts various fees—such as currency conversion fees, international fees, or adjustments—directly from your payouts before depositing funds into your bank. These are different from standard payment processing fees and can significantly impact your actual earnings. If payout fees are not recorded separately, your revenue may look lower than it really is, and expenses can be harder to track. By enabling this feature, you ensure that payout fees are posted independently in QuickBooks as expenses, giving you clearer visibility into true sales, more accurate financial reporting, and better insights into the overall cost of selling on Shopify.

So we’re excited to introduce a new feature that enhances your Shopify → QuickBooks integration by giving you the ability to download Shopify payout fees and post them separately in Webgility Online.

Note 1: This feature is available only to Webgility Online accounts integrated with Shopify as a sales channel and QuickBooks Online as an accounting system.

What’s New?

Just like how you view and post Orders and Refunds in the Sales section, a new Fees tab is now available. This allows you to:

  • View individual payout fee details in separate rows
  • Post payout fees directly into QuickBooks Online as an expense type, standalone transactions

How to Verify Payout Fee Values in Webgility Online

To confirm how Webgility Online calculates payout fees, you can cross-check directly in your Shopify account:

  1. Identify the payout date in Webgility Online.
    • Alternatively, click the Payout ID link in Webgility Online to be redirected straight to that payout in Shopify.
  2. In Shopify Admin, go to Settings > Payments > View Payouts.
  3. Select the payout that matches the same date.
  4. Open the payout report and review the list of fees.
  5. Add up all fees except those labeled “Charges.”
    • Note: “Charges” represent payment processing fees (credit card fees), which Webgility Online continues to post separately.
  6. The total of the remaining fees will equal the Payout Fee value you see in Webgility Online.

Note 2: Payment processing fees (e.g., credit card fees) will continue to be posted as before and are unaffected by this new feature.

Note 3: This feature is available only for Shopify and QuickBooks Online users who have set up a Transactional accounting method.

Setting up the feature:

  • In Webgility Online navigate to Sync Settings then go to Fees.
    • Under Settings for Posting Payout Fees enable the toggle button for “Enable posting payout fees”
    • Configure the Vendor for posting Shopify fees.
    • Then under “Set the Payment Date as”, here you will need to select Payout Date or Current date with the extensions available for days
    • Then under Payment Method, here you will need to select the appropriate payment method from your QuickBooks Online.
    • Then under Expense Account, here  you will need to select the appropriate expense account from your QuickBooks Online.
    • Then under Set the Payment Account as, you will need to select the required Other current asset/Bank account from your QuickBooks Online.
  • Once done then click on Save button at the bottom.

How it works:

  • The payout fees are downloaded automatically along with Shopify payouts.
  • In order to review the fees per payout, navigate to the Sales menu> Fees
    • Select the Payout and then click Post to QuickBooks. 

  • You can also set the automation for the same under Automation > Scheduler Rules > Expenses & Fees, Turn ON the toggle button for “Sync Payout Fees automatically” and then click on Save.

Once posted, a separate transaction will be created for the respective  Payout Fees as an expense in QuickBooks with the configured details.

Who Can Use This Feature?

  • Available to all customers on any Webgility Online package.
  • Only applicable if using the Transactional accounting method in your setup.