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Resolving Inventory Sync Discrepancies Between Shopify and QuickBooks Desktop in Webgility

This article helps Webgility Desktop users resolve inventory discrepancies between Shopify and QuickBooks Desktop when syncing through Webgility Desktop. The issue often arises when certain Shopify orders are marked as archived instead of canceled, preventing expected inventory updates. The article explains how to identify and correct the issue, along with best practices to prevent it from recurring.

Overview

You're seeing differences between your inventory quantities in QuickBooks Desktop and Shopify—even after syncing. Upon closer inspection, some of the affected orders in Shopify may be marked as archived, which doesn't adjust inventory in the same way that canceling an order would.

Symptoms You Might Notice:

  • Inventory levels in QuickBooks Desktop don’t match Shopify after a sync.
  • The mismatch started after a specific order was processed.
  • The order in Shopify is marked as archived, not canceled.
  • Refreshing or reconnecting the sync didn’t resolve the issue.

Reason

In Shopify, marking an order as archived removes it from the active order view but does not restock inventory like canceling an order does. As a result, QuickBooks Desktop doesn't receive the correct update, leading to inventory mismatches between systems.

How to Resolve the Issue

Step 1: Identify Archived Orders

  1. Log into your Shopify Admin.

  2. Click the Archived orders tab on the Dashboard

  3. Review the archived orders and look for any that may be connected to the inventory issue.

Step 2: Cross-Check the Order Status

  • Open the order that may have caused the issue.

  • Confirm if it’s archived and not canceled.

  • Determine whether the item(s) from that order were restocked or not.

Step 3: Correct the Order Status (If Needed)

  • If the order should be canceled (for example, the item was never shipped and was refunded), cancel the order instead of archiving it:

    • Click More Actions > Cancel Order in Shopify.

    • This will restock the item automatically (based on your store settings).

  • If the order was archived appropriately, make a note that it won’t impact inventory and adjust manually if needed.

Step 4: Resync Shopify and QuickBooks Desktop

  1. Open your Webgility Desktop.

  2. Click Refresh Data or run a manual sync.

  3. Wait for the sync to complete and check the inventory levels again.

Step 5: Reconnect Your QuickBooks Desktop Account (If Sync Issues Continue)

  • Test the QuickBooks Desktop connection in your Webgility Desktop setup.

  • Run another sync to confirm the issue is fully resolved.

Step 6: Verify Inventory Sync

  • Compare product inventory levels between Shopify and QuickBooks Desktop.

  • Double-check the order history to ensure everything looks consistent.

  • Make any manual adjustments if needed.