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.
5

Hi, @DKalenty

I think I understand your question, however, I want to clarify to be sure.

Shopify is the e-commerce platform, however we also provide an optional payment gateway called Shopify Payments. You can definitely use Shopify without using Shopify Payments. This means you can use Authorize.net as your primary payment gateway.

However, you can only have one primary payment gateway at a time. This means you can’t use Shopify Payments as well as Authorize.net.

Since the functionality you require is unavailable on Shopify Payments, your best route would be to continue using Authorize.net with your Shopify account. However, it’s also important to keep in mind that as Authorize.net is a third-party gateway you will be paying a slightly higher processing fee depending on your plan as you are subject to transaction fees. You can find out more information here.

I hope that makes sense!