How can I resolve double VAT application issue in my Swiss online store?

Accounting & Taxes
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Topic summary

A Swiss online store owner is experiencing a double VAT issue affecting domestic customers. The store’s base prices already include Swiss VAT and they sell both domestically and in Europe using IOSS.

The Problem:

  • European customers (e.g., from Italy) receive correct VAT treatment: Swiss VAT is subtracted, then destination country VAT is applied
  • Swiss domestic customers are incorrectly charged VAT twice: the base price already includes Swiss VAT, but VAT is being applied again at checkout

Current Status:

  • The issue exists in the live production store
  • A test store created in a “Shopify partner” account does not exhibit this problem
  • The store owner needs guidance on fixing the production environment

A community member requested additional details (tax settings, market configurations, and any overrides) to provide specific troubleshooting advice.

Summarized with AI on November 13. AI used: claude-sonnet-4-5-20250929.
1

Hi,

I’ve set up a shop in Switzerland a few months ago, we’re selling in our own country and in Europe.

VAT is being collected in our Switzerland market and in Europe (IOSS).

Our base prices INCLUDE the Swiss VAT.

A strange thing is happening:

  • a customer from Italy, for instance, gets the right VAT applied. First the Swiss VAT is subtracted, then the shipping destination VAT is added

  • a customer from Switzerland gets our VAT applied a second time (to the base price already including vat).

I’ve created a second test shop in a “Shopify partner” account and, as far as I can understand, this doesn’t happen anymore.

How can I fix this in the real shop (which is already in production)?

Thank you very much.

Cheers,

Andrea

2

HI Azicchetti,
Can you provide tax, market and overriides (if any) settings. Otherwise, it is not possible to advise.
Merry Christmas and Happy new year

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