Why does Shopify charge a 2% transaction fee for third-party providers?

Shopify Discussion

Topic summary

Shopify charges a 2% transaction fee when merchants use third-party payment providers instead of Shopify Payments. This fee applies on top of the 3-5% already paid to the third-party gateway.

Key Complaints:

  • Merchants in countries where Shopify Payments is unavailable (like South Africa) have no alternative but to use third-party providers
  • The 2% fee is perceived as charging for “doing nothing” since Shopify doesn’t process the payment
  • One user reported being charged the 2% even on declined transactions that generated $0 revenue

Merchant Response:

  • Multiple users have migrated or plan to migrate to alternative platforms like WooCommerce to avoid these fees
  • One merchant moved three shops away from Shopify, costing Shopify $75+ monthly in recurring revenue

Potential Workaround:

  • A user suggests using manual payment capture: authorize payments through the third-party gateway first, capture there, then manually mark orders as paid in Shopify
  • This method reportedly avoids the 2% Shopify fee but adds manual administrative work
  • The effectiveness of this workaround remains unconfirmed by other participants

The discussion reflects frustration with what merchants view as an unjustified fee structure, particularly for those without access to Shopify Payments.

Summarized with AI on October 25. AI used: claude-sonnet-4-5-20250929.
9

I agree 100%, this is completely unacceptable, especially when Shopify pay is not available and using a third party provider is the only option.

Personally I am busy testing a different platform and will migrate my shop away from Shopify soon because of this.

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