Using Authorize.net AND Shopify Payments?

Payments + Shipping & Fulfilment

Topic summary

A merchant is transitioning from a custom site to Shopify and wants to use both Authorize.net (as a gateway for manual billing outside the website) and Shopify Payments simultaneously. They currently charge customers an upfront registration fee plus recurring monthly fees for “block of the month” quilt kits, which they manually rebill through Authorize.net.

Key clarifications from support:

  • Shopify does not allow multiple primary payment gateways at once—merchants must choose either Shopify Payments or Authorize.net, not both
  • Alternative solutions include using draft orders for manual invoicing or setting up subscription apps (though the merchant finds these too expensive)
  • When using a third-party gateway like Authorize.net, Shopify charges an additional 2% transaction fee on top of the gateway’s own fees (totaling ~4%)
  • Switching to Shopify Payments alone would reduce total fees to 2.9% + $0.30 per transaction

Additional discussion points:

  • One participant notes that Authorize.net can function as just a gateway paired with independent processors, potentially offering cost savings
  • Support clarifies that within Shopify’s system, the processor and gateway must be the same entity

Unresolved issue: A merchant reports Apple Pay checkout errors after switching to Shopify Payments, which remains unaddressed in the thread.

Summarized with AI on November 12. AI used: claude-sonnet-4-5-20250929.
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Hi, @consolecowboy

Thanks for joining the conversation!

I absolutely understand that Authorize.net is a gateway and can work with other processors. However, Shopify itself does not allow you to have more than one main payment gateway. You can use Shopify Payments, or Authorize.net, not both.