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How to Resolve Duplicate Inventory Items in QuickBooks Desktop or QuickBooks Online

This article helps Webgility Desktop users identify and resolve duplicate inventory items in QuickBooks Desktop or QuickBooks Online that may interfere with inventory tracking, order posting, and synchronization with sales channels. It provides step-by-step guidance to manage overlapping product imports, resolve sync conflicts, and clean up legacy data to ensure accurate and consistent inventory records.

Step 1: Identify Duplicate Items in QuickBooks

Start by reviewing inventory data in QuickBooks:

  1. Open QuickBooks Inventory List

    • In QuickBooks Online:
      Go to Sales > Products and Services

    • In QuickBooks Desktop:
      Go to Lists > Item List

  2. Export Inventory Data (Recommended)

    • Export the product list to Excel or CSV for easier analysis.

  3. Scan for Duplicates

    • Use spreadsheet tools like Excel or Google Sheets.

    • Sort by Item Name or SKU.

    • Apply conditional formatting or use a formula like =COUNTIF(A:A, A2)>1 to highlight duplicates.

🧹 Step 2: Decide Which Duplicate to Keep

Once duplicates are identified, decide which version to keep:

  • Retain the item that has:

    • The most accurate SKU and product details

    • Valid sales history

    • Correct inventory quantity and integration links

  • All other duplicates should be either deleted or made inactive.

🧾 Step 3: Remove or Inactivate Duplicate Items

Depending on your QuickBooks version and company settings, you can either delete or make duplicates inactive:

If Deleting is Allowed:

  1. Select the duplicate item.

  2. Click Delete or Remove.

  3. Confirm the deletion.

  4. Verify the item no longer appears in your inventory.

If Deletion is Not Preferred or Available:

  1. Open the item record.

  2. Click Make Inactive.

  3. Confirm the change.

  4. Inactive items will be hidden from active inventory but retained in records for historical accuracy.

💡 Note: Making an item inactive does not delete it, but prevents it from appearing in standard inventory lists or being used in future transactions.

🔄 Step 4: Refresh Product Sync in Webgility 

After cleaning up duplicate items:

  1. In Webgility (or similar tool):

    • Go to Products > All Products

    • Click the Refresh icon

    • Choose Download from Scratch for both:

      • Your store platform (e.g., Shopify, BigCommerce)

      • QuickBooks