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How to Fix Invoices posted Incorrectly Marked as Paid in Webgility Desktop

This article helps Webgility Desktop users troubleshoot and resolve the issue where imported invoices are incorrectly marked as Paid, guiding them to correct the problem to maintain accurate financial records and smooth accounting workflows.

 Root Cause

This behavior is usually caused by the Payment Creation setting being enabled in your order sync settings setup. When this setting is turned on, Webgility Desktop automatically creates a payment record for each imported invoice, regardless of whether your customer has actually paid.

As a result, every invoice shows a "Paid" status by default—even if the balance is still outstanding.

Resolution Steps

Follow the steps below to stop Webgility Desktop from incorrectly marking unpaid invoices as paid:

Step 1: Access Webgility Desktop Settings

  1. Open your Webgility Desktop application.

  2. Navigate to Connections

Step 2: Disable the Payment Creation Option

  1. Select the relevant sales channel (e.g., Shopify, Amazon, WooCommerce).

  2. Go to Order Sync Settings > Under ‘Select the transaction type for posting orders’

  1. Go to the Setup & Uncheck or disable this option to stop Record payment.

  2. Click Save to apply your changes.

Step 3: Re-Sync Invoices

  1. Run a new sync or order import from your connected store.

  2. Check the status of the most recent invoices—only actually paid ones should now show as "Paid."

How to Verify the Fix

After changing the setting, review a handful of recent transactions:

  • Invoices for orders that were paid online or in person should correctly display as Paid.

  • Invoices for unpaid or pending orders should now correctly show as Unpaid or Open.