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Missing Shopify Fees When posting orders through Webgility Desktop

This article helps Webgility Desktop users who notice missing Shopify fees when downloading transactions into QuickBooks Desktop. This issue typically occurs when Shopify has not yet included fee data in the payout report at the time of sync. The article explains the root cause, how to verify the availability of payout data, and steps for re-downloading transactions once the data is accessible. It also shares best practices for monitoring payout timing and effectively managing recurring fee-related sync issues.

Overview

If you're noticing that Shopify fees aren’t appearing when downloading transactions into QuickBooks Desktop, you're not alone. This issue typically happens when the fees haven't yet been released in your Shopify payout reports at the time of the export. This guide walks you through why it happens and how to resolve it.


Issue

When downloading transactions into QuickBooks, some fees might appear to be missing. In most cases, this is because Shopify hasn’t yet posted those fees in the payout report for the related orders.

QuickBooks can only sync fees that are already included in Shopify’s payout reports.

Step-by-Step Troubleshooting

 1. Review the Timeline

Start by reviewing:

  • The date you exported transactions into QuickBooks.
  • The Shopify payout report for that same period.

If the fees aren’t listed in the payout report, they won’t show up in QuickBooks yet.

2. Understand How Shopify Posts Fees

It’s important to know:

  • Shopify does not always release fees immediately after an order is placed.
  • There can be a delay before the fees appear in the payout report, which is what Webgility uses to post to QuickBooks.

3. Check Payout Reports Again Later

We recommend the following:

  • Wait a day or two, then check the Shopify payout report again.
  • Once you see the expected fees listed in the payout summary, you're ready to retry the sync.

4. Redownload Affected Transactions

After confirming that the fees now appear in your payout report:

  • Go to Webgility Desktop >Orders
  • Select the affected date range.
  • Click Re-download/Resync to pull the updated data from Shopify.

QuickBooks will now receive the full transaction details, including any previously missing fees.

5. Verify in QuickBooks

Once the re-download is complete:

  • Open the corresponding transactions in QuickBooks Desktop.
  • Confirm that the Shopify fees now show correctly.