Shopify third-party payment fees: what another provider costs on each plan

Shopify charges a third-party transaction fee on orders paid through any payment provider other than Shopify Payments: 2% on Basic, 1% on Grow, 0.6% on Advanced, and 0.2% on Plus. It applies to the products minus discounts, plus tax and shipping, comes on top of the provider's own fee and the monthly plan, and isn't returned when you refund. A US store can't connect Stripe directly: Shopify's help says that where Shopify Payments is supported, Stripe won't be available to activate. On Flint the store runs on a commerce API with no monthly fee and no gateway fee: one rate per payment, with Stripe processing underneath.
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Shopify planPlan, billed monthlyThird-party transaction feeFee on $20,000 of monthly sales
Basic$392%$400
Grow$1051%$200
Advanced$3990.6%$120
PlusFrom $2,3000.2%$40

Flint charges 3.79% + 35¢ per card payment, which covers the Stripe processing, with no plan fee and no gateway fee on top. Checkout, orders, the catalog and inventory, discounts, fulfillment, returns, and the buyer account are included.

How Shopify calculates the fee

Shopify's billing help gives the formula for each billing period:

[(cost of products - discounts) + tax + shipping charges] x rate

  • It includes tax and shipping. On Basic, a $50 order with $4 of tax and $6 of shipping is charged 2% of $60, $1.20, before your provider's fee.
  • It's on top of the provider. Shopify's help says the fees "are in addition to processing fees charged by your third-party payment provider."
  • Refunds don't return it. "Third-party transaction fees aren't returned to you when you issue an order refund."
  • Turning on Shopify Payments doesn't remove it for orders that go through another gateway. Orders paid with Shopify Payments, Shop Pay, and manual methods such as cash on delivery carry no third-party fee, and PayPal is exempt when Shopify Payments is your primary provider.
  • Gift cards and store credit count on stores created on or after May 12, 2025, for the part of the order they pay.

What a month costs with a third-party provider on Shopify

Take a store with $20,000 a month in sales: 400 orders averaging $50, each total including tax and shipping, all paid through a third-party provider charging 2.9% + 30¢ per order. That provider fee is $580 plus $120, or $700 a month.

SetupPlanThird-party feeProcessingTotal per month
Shopify Basic with a third-party provider$39$400$700$1,139
Shopify Grow with a third-party provider$105$200$700$1,005
Shopify Advanced with a third-party provider$399$120$700$1,219
Flint$0$0$898$898

Flint's $898 is 3.79% of $20,000, $758, plus 35¢ on 400 orders, $140. Turning on Flint's automatic US sales tax adds 0.50% to payments that carry tax, at most $100 here, for $998. None of the rows include apps, themes, or Shopify's own tax pricing. For your own store, Shopify's cost is the plan, plus the plan's rate and your provider's percentage on sales, plus the provider's fixed fee per order. Flint is 3.79% of sales plus 35¢ per order, and above $50,000 a month you can ask Flint for negotiated terms.

Why you can't keep Shopify and swap the checkout

The usual next idea is to keep Shopify for the catalog and send buyers to a cheaper checkout. Shopify's API terms close that door: section 2.3.18 says that, without Shopify's express written authorization, an API user may not "use an alternative to Shopify Checkout for checkout or payment processing for Shopify Merchants." Headless Shopify storefronts end the same way: Shopify's docs say the Cart API "redirects to Shopify's Web Checkout."

So the choice is between Shopify Payments and leaving the fee behind with the platform. Flint takes the second path: the store's backend moves to Flint, and your storefront keeps its design. The headless Shopify checkout page walks through it for a Hydrogen, Next.js, or Remix storefront.

Running the store on Flint

Flint is a commerce API for ecommerce with a hosted checkout and a buyer account. Export your products from Shopify as a CSV and create each one with its options, variants, and stock. Keeping the Shopify handle in metadata lets your existing URLs resolve:

cURL
curl -X POST https://api.withflintpay.com/v1/products \
  -H "Authorization: Bearer YOUR_API_KEY" \
  -H "Idempotency-Key: import-shopify-tee-classic" \
  -H "Content-Type: application/json" \
  -d '{
    "name": "Classic tee",
    "product_type": "physical",
    "metadata": {"shopify_handle": "classic-tee"},
    "options": [{
      "name": "Size",
      "values": [
        {"value": "M"},
        {"value": "L"}
      ]
    }],
    "variants": [
      {
        "sku": "TEE-CLASSIC-M",
        "unit_price_money": {"amount": 2800, "currency": "USD"},
        "line_item_tax_category": "clothing",
        "selected_options": [{"option_name": "Size", "value": "M"}],
        "inventory_item": {"name": "Classic tee, M", "sku": "TEE-CLASSIC-M"}
      },
      {
        "sku": "TEE-CLASSIC-L",
        "unit_price_money": {"amount": 2800, "currency": "USD"},
        "line_item_tax_category": "clothing",
        "selected_options": [{"option_name": "Size", "value": "L"}],
        "inventory_item": {"name": "Classic tee, L", "sku": "TEE-CLASSIC-L"}
      }
    ]
  }'

The cart becomes an order. Flint prices each line from the catalog, applies promotions, calculates US sales tax for the address, and holds the stock when the buyer pays. Checkout is Flint's hosted page, which takes cards, Apple Pay, Google Pay, ACH debit, and Affirm, or your own page with Stripe Elements:

Shell
# The cart is an order. Send the buyer to hosted checkout with your
# shipping and pickup methods; or pay it on your own page with Stripe Elements.
curl -X POST https://api.withflintpay.com/v1/checkout-sessions \
  -H "Authorization: Bearer YOUR_API_KEY" \
  -H "Idempotency-Key: checkout-cart-5521" \
  -H "Content-Type: application/json" \
  -d '{
    "order_id": "ord_1kmn0aExample",
    "delivery_method_ids": ["dmet_1kmn0aShipping", "dmet_1kmn0aPickup"],
    "redirects": {"success_redirect_url": "https://shop.example.com/thanks"}
  }'
On ShopifyOn Flint
Products and variantsProducts with options and variants, POST /v1/products
InventoryStock per location, held at payment
Discount codes and automatic discountsPromotions with codes, automatic discounts, and stacking rules
Shipping rates and local pickupDelivery methods: rate tables, free shipping thresholds, pickup, local delivery
CheckoutHosted checkout, or your own page with Stripe Elements
Customer accountsA hosted buyer account with order history and returns
Returns and refundsReturns with policies and restocking; refunds by line item
SubscriptionsPlans that ship, with each renewal as an order

Shopify with a third-party provider, and Flint, side by side

Shopify with a third-party providerFlint
Monthly plan$39 to $399, Plus from $2,300None
Fee for the processor you use2% to 0.2% by plan, on tax and shipping tooNone; Stripe processing is built in
Card processingYour provider's fee, such as 2.9% + 30¢Included in 3.79% + 35¢
Checkout for a headless storefrontRedirects to Shopify's web checkoutHosted checkout or your own page

Who Flint is built for

Flint is for US businesses that sell on their own website or app and get paid in US dollars. Buyers can pay from anywhere with a card. It is an API and hosted checkout, not a store builder: there are no themes or app store, and your storefront is your own code or site. Flint handles online and in-app payments, not card readers.

Questions, answered

How much does Shopify charge for third-party payment providers?

2% on Basic, 1% on Grow, 0.6% on Advanced, and 0.2% on Plus, for orders paid through a provider other than Shopify Payments. The fee is on top of the provider's own processing fee and the monthly plan, and Shopify doesn't return it when you refund an order.

Does Shopify charge a fee for using Stripe?

A US store can't use Stripe as its Shopify payment gateway. Shopify's help says that where Shopify Payments is supported in your country, Stripe won't be available to activate, and standalone Stripe isn't an alternative even if you can't activate Shopify Payments. Orders paid through any other third-party provider carry Shopify's fee for your plan: 2% on Basic, 1% on Grow, 0.6% on Advanced, or 0.2% on Plus, on top of the provider's own processing fee.

What is the Shopify third-party transaction fee calculated on?

Shopify's billing help gives the formula: the cost of products minus discounts, plus tax, plus shipping, multiplied by your plan's rate. So the fee applies to the tax and shipping you collect, not only to the merchandise.

How do I avoid Shopify's third-party transaction fee?

Within Shopify, accept payments through Shopify Payments; orders paid with Shopify Payments, Shop Pay, or manual methods such as cash on delivery carry no third-party fee. Outside Shopify, run the store on a commerce API that includes payments. Flint has no monthly fee and no gateway fee: cards cost 3.79% + 35¢ per payment, with Stripe processing included.

Can I keep Shopify and use Flint as the checkout?

No. Shopify's API terms don't allow an alternative to Shopify Checkout for Shopify merchants without Shopify's written authorization. Flint replaces the store's backend instead: products, variants, stock, orders, tax, and checkout move to Flint, and your storefront keeps its design.

Does Flint have themes or a store builder?

No. Flint is a commerce API with a hosted checkout, payment links, and a buyer account. Your storefront is your own site or app, such as a Next.js or Hydrogen front end, and it reads products and creates orders through the API.

Is Flint a good alternative to Shopify?

For a US business with its own storefront that wants to stop paying a monthly plan and a gateway fee, yes. Flint includes the catalog with variants, inventory held at payment, promotions, shipping and pickup, returns, and a hosted checkout in one per-payment rate, with automatic US sales tax (+0.50% on taxed payments) and subscriptions (+0.40%) as add-ons. If you rely on Shopify's themes and app store, Flint doesn't replace those.

Sources

All sources accessed October 15, 2026.