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Troubleshooting Missing VAT on Imported Invoices via Webgility Desktop

This article helps Webgility Desktop users troubleshoot issues where VAT taxes are not populating in QuickBooks Desktop across multiple integrated channels (such as Amazon GB, BigCommerce, eBay, and Magento). It explains how the problem often stems from improperly synced tax settings and provides steps to resolve missing tax data on imported invoices.

Overview

This article outlines the troubleshooting process for situations where VAT taxes are not populating in QuickBooks across multiple integrated channels (e.g., Amazon GB, BigCommerce, eBay, Magento). The issue commonly arises when tax settings do not sync properly, leading to missing tax data on imported invoices.

Cause Analysis

Possible causes for taxes not appearing include:

  • Incorrect VAT tax rate configuration in store platforms or QuickBooks
  • Tax settings mismatch (e.g., exclusive vs. inclusive)
  • Store/account-level integration settings not synced
  • Data sync errors between stores and QuickBooks

Step-by-Step Troubleshooting Guide

1. Verify Store Tax Settings

  • Check each store (Amazon GB, BigCommerce, eBay, Magento) for correct VAT rates.
  • Ensure the tax rates match your region's requirements.
  • Confirm if taxes are set as inclusive or exclusive.

2. Review QuickBooks Tax Configuration

  • Go to Taxes in QuickBooks.
  • Check that VAT rates are active and accurately reflect the latest updates.
  • Confirm QuickBooks is set to the same tax modality (inclusive/exclusive) as your stores.

3. Test Invoice Import

  • Conduct a test transaction from each store.
  • Import the transaction to QuickBooks via Webgility.
  • Observe if VAT/taxes populate correctly.

4. Sync and Integration Settings

  • In Webgility, review mapping for tax fields between stores and QuickBooks.
  • Re-map or refresh tax settings if necessary.
  • If available, trigger a manual sync.

5. Isolate the Issue

  • Temporarily set the store/platform to exclude tax settings.
  • Re-import recent invoices and check QuickBooks for tax visibility.
  • Switch back to original settings and test again.