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How to Reauthorize Shopify Connection to Fix Order Download Problems in Webgility Desktop

This article helps Webgility Desktop users troubleshoot issues related to missing or failed Shopify order downloads. Such sync problems can disrupt critical business operations like order processing, accounting integration, and reporting accuracy. The guidance is particularly useful for users connecting a Shopify store for the first time, reauthorizing after password or permission changes, or addressing reports of incomplete or missing order data.

Overview

If orders from Shopify aren’t showing up in Webgility Desktop, this guide walks you through how to identify the issue, perform key troubleshooting steps, and restore order synchronization. These steps apply whether you’re missing recent orders, seeing sync failures, or facing outdated API issues.

Why This Happens

Shopify orders may not download into Webgility Desktop for a few common reasons:

  • A temporary sync/API disruption between Shopify and Webgility

  • Expired, revoked, or missing Shopify credentials/permissions

  • Using an outdated Webgility version incompatible with the latest Shopify API

Step-by-Step Troubleshooting Guide

Step 1: Confirm Your Webgility Version

  • In Webgility Desktop, go to Help > Check for Updates

  • Verify that you’re running version 9.9.2 or later

  •  If you are not on the latest version:

Step 2: Test with a New Shopify Order

  • Ask your team (or customer) to create a test order in Shopify

  • In Webgility, go to Orders > Get Orders > Shopify

  • Wait for the sync to complete and check if the new order appears

Step 3: Backdate the Order Download (For Missing Orders)

If the test order works, but older ones are still missing:

  • Go to Integration > Connections > Sales Channels > Settings > Backdate Orders

  • Choose a date range that includes the period of the missing orders

  • Click Backdate to redownload historical Shopify orders

  • Once complete, review your orders list to confirm recovery

Step 4: Reauthorize Your Shopify Store (If Sync Still Fails)

If you're still experiencing issues after the steps above:

  1. Navigate to Connections > Sales Channels > Manage Sales Channel

  2. Locate your Shopify store and choose Disconnect or Remove Authorization

  3. Reconnect the store by selecting Add or Reauthorize Shopify

    • You’ll be prompted to log into Shopify and approve the Webgility app

  4. After reauthorization, go back to Orders > Get Orders or Backdate Orders and retry sync

Final Verification Checklist

Before closing out the issue, confirm the following:

  • Orders are now syncing correctly from Shopify to Webgility

  • No error messages are appearing during sync

  • You are using Webgility version 9.9.2 or later

  • (Optional) Historical orders were successfully recovered via Backdate