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Orders Missing in QuickBooks When Using Webgility Desktop

This article helps Webgility Desktop users troubleshoot situations where certain posted orders are not appearing in QuickBooks Desktop. It provides a step-by-step guide to identify the root cause and resolve the issue, particularly when posting orders from multiple sales channels into QuickBooks Desktop through Webgility Desktop.

How to Resolve Missing Orders

1. Confirm Order Is Posted in Webgility Desktop

Start by checking whether the order was successfully posted:

  • Open Webgility Desktop

  • Go to: Orders > Posted Orders

  • Search for the missing order

  • Take note of the order ID, order date, and store name

If the order isn’t listed, it may not have downloaded. Use manual download options described at the end of this article.

2. Check Sales Channel Settings

Ensure Webgility is connected to the correct Sales Channel settings are correct:

  • Go to: Connections > Sales Channel > Manage Connection

  • Verify that:

    • Sales Channel credentials are accurate

    • Posting settings (e.g., order status, date range) are configured to include the desired orders

    • All intended stores are included in the sync

4. Search for Orders in QuickBooks

The order may exist in QuickBooks but not be immediately visible:

  • Open QuickBooks and the correct company file

  • Use the Search bar or run Sales Reports (e.g., Sales by Order or Sales by Item)

  • Look under Sales Orders, Invoices, or Sales Receipts, depending on how orders are posted

  • Try different date ranges or search using part of the order number

  • Be aware that order formatting may differ slightly between stores

Optional: Manually Download Missing Orders into Webgility

If the order isn’t in Webgility yet, try manually downloading it using one of these methods:

Download by Date Range

  • In Webgility, click the dropdown on the Get New Orders button

  • Select Orders by Range

  • Enter the appropriate date range

  • Click Get New Orders

Download by Order ID

  • Click the dropdown on Get New Orders

  • Select Orders by ID

  • Enter the order number(s)

  • Click Add, then Get Orders

Tip: In some sales channels like Shopify, the order ID may be different from the order number. You can find the ID in the URL when viewing the order in the store admin.