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Fixing Inventory Sync Issues Between Shopify and QuickBooks Online After API Changes

This article helps Webgility Desktop users in identifying and addressing inventory mismatches such as incorrect cost or quantity when syncing products between Shopify and QuickBooks Online using Webgility Desktop. It guides users in understanding the root cause of the issue, which stems from recent API changes made by Shopify and/or QuickBooks Online. 

Overview

If you've noticed discrepancies in item costs or quantities after syncing inventory from Shopify to QuickBooks Online using Webgility Desktop, you're not alone. Recent changes to Shopify and QuickBooks APIs have impacted how inventory data is mapped and transferred. This article explains the cause and outlines the steps to resolve the issue.

What’s Causing the Problem?

  • Recent API updates from Shopify or QuickBooks, or both, have altered how inventory data syncs.

  • These changes may result in incorrect cost or quantity values for synced items in QuickBooks.

What’s Being Done

  • A permanent fix has been developed and successfully tested in staging.

  • The fix is included in an upcoming Webgility Desktop update, scheduled for release on June 19.

  • After the update, inventory data should sync accurately across systems.

What You Can Do Now

Step 1: Check for Inventory Discrepancies

  1. Open Webgility Desktop.

  2. Perform an inventory sync from Shopify to QuickBooks.

  3. Review a few sample items and compare cost and quantity values across both platforms.

  4. Note any mismatches for future comparison.

Step 2: Apply a Temporary Workaround

While waiting for the update:

  • Manually update incorrect cost or quantity values in QuickBooks.

  • Or, export inventory reports from both systems for manual cross-checking.

After the Update—Steps to Follow

Step 3: Update Webgility Desktop

  1. Launch Webgility Desktop.

  2. Go to the menu: Help > Check for Updates. You can refer to this article as well.

    Update Webgility Desktop Using the “Check for Updates” Option

  3. Download and install the June 19 update (or later).

Step 4: Test Inventory Sync Again

  1. Once updated, run a new inventory sync from Shopify to QuickBooks.

  2. Recheck the previously mismatched items.

  3. Confirm that item costs and quantities now match correctly between both platforms.

Step 5: Keep Webgility Desktop Updated

To avoid future issues:

  • Regularly check for updates by navigating to Help > Check for Updates in the Webgility Desktop menu.

  • Staying the current version ensures compatibility with evolving Shopify and QuickBooks APIs.

In Summary

Inventory mismatches were caused by recent API changes from Shopify and QuickBooks. A fix is coming in the June 19 update to Webgility Desktop. In the meantime, you can manually review and adjust values as needed. Once updated, you’ll be able to sync inventory data accurately again—ensuring consistency across your platforms.