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How to Fix Shopify Overselling Caused by Inventory Discrepancies in Webgility Online

This article explains why Shopify may display incorrect inventory quantities when synced from QuickBooks through Webgility Online. It covers two common causes of inventory discrepancies: orders remaining in the Flag tab due to missing QuickBooks item mappings and refunds processed for items that customers did not physically return. It walks you through resolving flagged orders, correcting inventory quantities for non-returned items, and running an inventory sync to ensure Shopify reflects the accurate stock available in QuickBooks.

 Why Does Shopify Show Incorrect Inventory?

Two common situations can cause QuickBooks to show more inventory than you actually have.

1. Orders Stuck in the Flag Tab

Orders containing products that are not mapped to QuickBooks items may appear in the Flag tab in Webgility Online.

Until the missing products are mapped and the orders are successfully posted to QuickBooks, inventory quantities are not reduced for those orders.

As a result, QuickBooks continues to show the previous stock quantity, which Webgility Online may sync to Shopify.

Example: If you have 10 units in QuickBooks and receive an order for 3 units, but the order remains in the Flag tab, QuickBooks will continue to show 10 units instead of the actual remaining quantity of 7.

2. Refunds for Items Not Returned

When a refund is processed for an item that the customer does not return, the inventory should not increase.

However, depending on the refund posting configuration, QuickBooks may add the refunded quantity back to inventory.

This creates a discrepancy between the quantity in QuickBooks and the actual stock available on your shelf.

Steps to Correct the Inventory Discrepancy

Step 1: Review Orders in the Flag Tab

  1. Log in to Webgility Online.
  2. Navigate to Orders > Flag.
  3. Review the orders that have not been posted to QuickBooks.
  4. Identify products that are missing their QuickBooks item mappings.

Step 2: Map Products and Post Flagged Orders

Once the missing products are mapped:

  1. Select the flagged orders.
  2. Complete the required mapping.
  3. Post the orders to QuickBooks.
  4. Verify that the orders have posted successfully.

Posting these orders ensures that QuickBooks reflects the inventory reduction for the sold items.

For reference, visit the article Resolving the “Product Not Mapped to an Accounting Item” Order Flag in Webgility Online 

For mapping missing products, refer to How to Map Products While Posting Orders in Webgility Online.

Step 3: Correct Inventory for Refunds Without Returns

If you refunded a customer but did not receive the product back, verify whether QuickBooks increased the item's inventory quantity when the refund was posted.

To correct this:

  1. Locate the corresponding refund in QuickBooks.
  2. Confirm whether the refunded quantity was added back to inventory.
  3. If the item was not returned, adjust its on-hand quantity in QuickBooks to reflect the actual physical stock.

For instructions on processing refunds, refer to How to Post Refunds in Webgility Online.

Note: Only adjust inventory for items that were not physically returned. If an item was returned and is available for resale, its quantity should remain included in your inventory.

Step 4: Run Inventory Sync and Verify Shopify Quantities

After correcting the flagged orders and inventory quantities in QuickBooks you can run inventory sync in two ways

  • Running manual product sync

For detailed instructions please visit: How to sync Inventory in Webgility Online  

  • Setting up Automation for the same

For detailed instructions please visit: Set Up Automation for inventory sync in Webgility Online 

Webgility Online typically syncs inventory approximately every 15–20 minutes.