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How to Resolve Missing Shopify Orders in Webgility Desktop

This article helps Webgility Desktop users identify and resolve missing Shopify orders in Webgility Desktop, particularly those that are manual, have zero value, or are marked as check payments. It provides guidance on diagnosing the issue, correcting it, and implementing best practices to prevent it from happening in the future.

Overview

If you’ve noticed that some of your Shopify orders are missing, especially those that are manual, have zero value, or are marked as check payments, you’re not alone. This article guides you through identifying the issue, resolving it, and preventing it in the future using Webgility.

Issue: 

You may find that a batch of orders doesn't appear in your Shopify order history or within Webgility. These missing orders are commonly:

  • Manually created
  • Have zero-dollar totals
  • Use check or manual payment methods

These types of orders can sometimes be excluded during syncs or data transfers if not properly recorded.

Steps to Identify and Resolve the Issue

1. Download and Review Order Data

Start by exporting your full order history from Shopify. This helps confirm which orders are present and which may be missing.

2. Share JSON Exports

If specific orders appear to be missing, you’ll need to export the JSON data for those orders directly from Shopify. Webgility Support will use this to verify if the order data is complete or incorrectly formatted.

Tip: You can get JSON data using the Shopify Admin API or by exporting from your admin console if enabled.

What You Should Do Next

  • Monitor for Additional Issues: Keep an eye on your order list. If more orders go missing, document them immediately.

Best Practices Going Forward

To avoid similar issues in the future:

  • Export JSON data for any missing or suspicious orders.

  • Stay informed: Always ask for updates and provide timelines when reaching out to Support.

  • Check order integrity regularly, especially after bulk imports or making changes to your payment settings or order workflows.