This setting tries to answer a question: are the prices Shopify sends to Junipeer inclusive or exclusive of VAT?
Checked (inclusive) → the price on each line already contains VAT. E.g. 100 SEK means 80 SEK net + 20 SEK VAT. Junipeer needs to strip VAT out before posting to Fortnox.
Unchecked (exclusive) → the price is net. Fortnox adds VAT on top.
Getting this wrong causes double VAT or missing VAT on every single invoice — one of the most common setup errors. It depends entirely on how the eCom platform is configured. Shopify in Sweden typically sends prices inclusive of VAT for B2C storefronts, but this can vary.