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How to Resolve Sales Tax Inconsistencies in Webgility Desktop with QuickBooks Online and Shopify integration

This article helps Webgility Desktop users in troubleshooting and resolving sales tax inconsistencies when integrating Webgility Desktop with QuickBooks Online, especially in multi-channel setups using Shopify and BigCommerce. It provides a systematic approach to address issues such as inaccurate sales tax values on orders, incorrect tax breakdowns, and inconsistent mapping of the “Multiple State Tax” code. The guide also covers how third-party integrations may impact tax data flows and offers solutions to maintain accurate tax reporting and compliance.

Overview

Sales tax inconsistencies may occur when integrating Webgility with QuickBooks Online (QBO), particularly in multi-channel environments using Shopify and BigCommerce. Correct sales tax mapping and reporting is crucial for accurate financials and compliance.

This guide outlines how to systematically troubleshoot and resolve ongoing issues related to sales tax data—especially with the 'Multiple State Tax' code—after order posting.

Common Issues Identified

  • Orders posted from Shopify/BigCommerce to QuickBooks do not reflect accurate sales tax values.
  • Tax breakdowns (state, county, city, district) merge incorrectly or lose detail in QBO.
  • The 'Multiple State Tax' code does not map taxes consistently, causing reporting mismatches.
  • Third-party integrations may be conflicting with tax data flows or overwriting expected mappings.

Pre-Troubleshooting Checklist

  • Ensure latest versions: Confirm Webgility, QuickBooks Online Connector, and sales platform apps are up-to-date.
  • Document the problem: Gather screenshots, affected order samples, tax settings in WebDynamics and QBO.
  • List active third-party apps: Document all integrations touching sales, tax, and order data in Shopify/BigCommerce.

Step-by-Step Troubleshooting

1. Review Tax Configuration in WebDynamics

  • Go to Webgility, Connections > Accounting/POS/ERP > Sync Settings.
  • Ensure each external sales tax (state, city, county) used by Shopify/BigCommerce is mapped to a corresponding QBO tax code.
  • Check that the 'Multiple State Tax' code is only used when absolutely necessary. Avoid catch-all codes, which reduce reporting detail.

2. Verify QuickBooks Online Tax Setup

  • In QBO, navigate to Taxes > Sales Tax Settings.
  • Check that all expected tax codes are present and active.
  • For states with complex tax rules, make sure tax agencies/locations are set up.

3. Examine Integration Settings

  • In Webgility, disable any unnecessary third-party plugins that affect orders or taxes.
  • Confirm data sync frequency and identify any logs showing failed syncs or error codes.

4. Test Order Export

  • Create a test order in Shopify/BigCommerce with multi-state tax (if applicable).
  • Post to QBO and observe:
    • Are all tax components itemized correctly?
    • Is the correct tax code assigned?
    • Are discrepancies logged in either platform?
  • Document observed results with screenshots.

5. Analyze Data Flow and Logs

  • Check integration logs in Webgility and QBO for errors, warnings, or failed tax code mappings during order posting.
  • Cross-verify totals in posted orders with the original order data.