Skip to content
  • There are no suggestions because the search field is empty.

How to fix  Inventory Sync Issues Between Shopify and QuickBooks in Webgility Desktop

This article helps Webgility Desktop users through the process of mapping unmatched products, resolving discrepancies, and maintaining consistent data across platforms. This ensures sales, inventory, and accounting data remain synchronized between sales channel and QuickBooks Desktop.

Accurate product mapping in Webgility ensures that your sales, inventory, and accounting data stay in sync between your online store and QuickBooks. This step-by-step guide walks you through mapping unmatched products, resolving discrepancies, and ensuring synchronization across all platforms.

Test your sales channel and QuickBooks company file connections:

1. To test the Sales Channel connection: Help Article.

2. To test the QuickBooks connection: Help Article

Step-by-Step: How to Map Products in Webgility

1. Review Unmapped Products

  • Navigate to Products > Missing in QuickBooks.

  • You'll see a list of products available in your online store but not matched with any items in QuickBooks.

2. Map Products

  • Select one or more products and click the Map Product button.

  • You will be prompted to choose between:

    A. One-Click Mapping

  • Choose to match the product SKU from your store to:

    • Item Name/Number

    • Manufacturer Part#

    • Barcode

    • Sub-item of (for category-based structures in QuickBooks)

  • Select the relevant QuickBooks field and click Continue.

    B. Auto-Recommendation

  • Webgility will search QuickBooks for SKU, description, or barcode matches.

  • Select the suggested QuickBooks product and click Map Product.

    C. Manual Mapping

  • If no matches are found, click Search for Correct Match, search by name or SKU, and manually link to the correct QuickBooks item.

3. View or Remove Mappings

  • Go to Products > All Products > Filter: Mapped to view successfully mapped products.

  • To remove incorrect mappings, select the product and click the Remove Mappings icon.

Note: If mapped products are displayed in red, it indicates invalid mapping. Unmap and remap those products to correct the issue.

4. Check for Mapping Discrepancies

To proactively manage your mappings:

A. Export Product Lists

  • Export product data from:

    • Webgility: Products > Export to CSV

    • QuickBooks: List > Item List > Export List

    • Your Online Store (e.g., BigCommerce): Products > Export

B. Compare Product Details

  • Use a spreadsheet to cross-check SKUs, names, and statuses.

  • Highlight:

    • Missing items in one system

    • SKU mismatches

    • Inconsistent naming

5. Sync Missing Products or Fix Discrepancies

Add Missing Items

  • Add the missing product to your online store or QuickBooks (depending on the source of truth).

  • After adding, download updated data into Webgility.

Update SKU/Naming

  • Adjust inconsistent SKUs or names in the primary platform.

  • Then refresh product data in Webgility using:

    • Products > All Products > Store > Refresh icon > Download from Scratch

6. Verify Automation and Sync Settings

To avoid automated overwrites:

  • Go to Settings > Automation Rules

  • Disable unwanted auto-sync rules until mappings are verified.

  • Confirm the correct "Master Data" source under Product > Settings > Sync Settings.

    Best Practices

    • Always create products first in the platform that serves as your 'source of truth'.

    • Periodically audit your mapped items using Webgility reports or exports.

    • Only enable auto-sync when product mapping is fully reviewed and verified.