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 Stop Shop App Marketplace Tax From Posting to QuickBooks in Webgility Desktop

Turn on the right marketplace-tax setting, reconnect your Shopify store, and re-download affected orders so Shop app tax stops landing in QuickBooks.

Overview

Shopify's Shop app collects and remits sales tax for marketplace-liable orders. When Webgility Desktop posts those orders to QuickBooks with the tax line attached, that marketplace tax inflates your Sales Tax Payable account. This article explains how to turn on the correct setting, confirm the sales channel is reporting marketplace tax, and clean up orders that already posted.

When This Applies

Use these steps if your Shopify orders are posting to QuickBooks Desktop through Webgility Desktop, and Shop app orders (or other channel-liable orders) are still carrying their tax amount into QuickBooks even though you intend Shopify to handle that tax itself.

Why This Happens

Webgility recognizes an order's tax as marketplace tax only when the setting Do not record marketplace tax in QuickBooks is on and the Shopify connection is passing the channel-liable tax field correctly. If the setting is off, Webgility treats the tax as regular sales tax and posts it to your chosen tax item. Older Shopify REST API connections also miss the marketplace-tax field on some orders, so switching to Shopify's current GraphQL API through a fresh reconnection restores the right data flow.

Important Note

Changing this setting affects only orders downloaded after the change. Orders already in Webgility keep the data they came in with, so you need to re-download the affected orders after the fix to clear the tax from new postings.

Steps to Stop Shop App Marketplace Tax From Posting to QuickBooks

  1. Open Webgility Desktop and go to Connections > Accounting > Sync Settings > Sales Tax.
  2. Confirm the primary tax rule. Keep Record sales tax calculated from Sales Channel as a line item selected if that matches your QuickBooks tax item setup — see the Sales Tax posting settings article for the full field map.
  3. Turn on Do not record marketplace tax in QuickBooks, click Save, and close the panel.
      
  4. Reconnect the Shopify sales channel from Connections > Sales Channels > Manage Sales Channel, click the Edit Connection pencil, and run Connect to Shopify. This refreshes the connection to Shopify's current API so marketplace-tax data arrives on each order — step-by-step guidance is in Reconnect a Shopify store in Webgility Desktop.
  5. Unsync the affected Shop app orders that already posted — this prevents a duplicate post to QuickBooks when they come back in — then select them, right-click, and choose Re-download Order. If re-download has not been enabled on the sales channel yet, turn it on first at Connections > Sales Channels > Settings > Order Processing by selecting Yes for Do you want to use the re-download order feature and clicking Save & Continue. The Order Re-download in Webgility Desktop article covers all three re-download methods (right-click, More Actions > Re-download order, and the Redownload icon on the order details screen). New Orders > Download Orders is for fetching new or missing orders only and will not refresh orders already in Webgility.
  6. Repost the orders from New Orders. The Shop app tax will stay in the Marketplace Tax field in Webgility and will not post to the QuickBooks tax item.

Key Recommendation

Before you repost a large backlog, pick two or three Shop app orders, repost them, and open the resulting QuickBooks transaction to confirm the tax line is gone from the sales tax item. Once that test is clean, run the full re-download for the date range you need to correct.

Additional Support

If Shop app orders still carry tax to QuickBooks after the reconnection and re-download, open a Webgility support ticket with two sample order numbers and a screenshot of the posted QuickBooks transaction so support can trace the tax field on each order.