STRIPE INTEGRATION AT A GLANCE
COMPLEXITY
Medium
METHOD
TYPICAL SETUP
1 week
WHAT WE DO
Set up Stripe for the cases Shopify Payments does not cover: B2B invoicing, subscriptions outside Shopify, marketplaces and custom checkouts on headless builds.
CATEGORY
Payments
SETUP BY PLATFORM
How we set up Stripe
Shopify
Stripe on Shopify (Payments (via Shopify)): Set up Stripe for the cases Shopify Payments does not cover: B2B invoicing, subscriptions outside Shopify, marketplaces and custom checkouts on headless builds.
Shopify store builds →Shopify Plus
On Shopify Plus (Payments + B2B): everything in Shopify, plus the Plus-only hooks (checkout extensions, B2B, Launchpad) where Stripe can use them.
Hydrogen
On a headless storefront (Hydrogen, Astro or Next.js) we connect Stripe through Stripe API and own the event and data mapping ourselves.
USE CASES
What teams use it for
B2B invoicing
Net-terms invoices and ACH for wholesale accounts.
Custom billing
Memberships, deposits and instalments outside the standard checkout.
Headless checkout
Stripe Checkout or Elements on Astro and Next.js builds where Shopify checkout is not used.
BEFORE YOU ADD IT
What to watch out for
FEES
Third-party gateway fees
Using Stripe instead of Shopify Payments adds transaction fees on most plans.
COMPLIANCE
PCI scope
Custom checkouts widen PCI scope. Use Stripe-hosted elements.
RECONCILIATION
Two ledgers
Stripe and Shopify payouts need reconciliation in your accounting tool.
05
Stripe on Shopify, in practice
On a standard Shopify store, Stripe is already there: Shopify Payments runs on Stripe infrastructure, so there is nothing to integrate. Stripe becomes a project when the store is headless, sells something Shopify Payments does not support, or runs subscriptions and invoicing outside Shopify.
On Hydrogen and Next.js builds we still route the cart through Shopify checkout wherever possible, because Shop Pay and checkout extensibility are worth more than custom payment UI. Stripe directly is for the exceptions: B2B invoicing with net terms, donation flows on nonprofit sites, service deposits, or marketplaces that need Connect. In those cases we build the payment flow, write the webhook handlers that create or update Shopify orders, and reconcile payouts.
The thing to avoid is two payment systems with two records of the same sale. Every Stripe charge we set up writes back to Shopify as an order or a customer note, and finance gets one export. If you are on Shopify Payments and someone proposes replacing it with Stripe, the honest answer is usually no.
Should we use Stripe or Shopify Payments?
Shopify Payments stays the default for checkout and already runs on Stripe infrastructure. Stripe directly is for exceptions such as B2B invoicing, custom billing or headless flows. Replacing Shopify Payments with Stripe is usually not worth it.
Can Stripe handle B2B net terms?
Yes. Stripe is how we handle B2B invoicing with net terms and ACH for wholesale accounts. Every charge writes back to Shopify as an order or customer note, so finance gets one export.
Does Stripe work with Hydrogen?
Yes, through the Stripe API. We still route the cart through Shopify checkout wherever possible, because Shop Pay and checkout extensibility are worth more than custom payment UI.
How do we reconcile Stripe and Shopify payouts?
We write webhook handlers that create or update Shopify orders and reconcile payouts. Every Stripe charge writes back to Shopify, so finance gets one export instead of two ledgers.
You've reached the end, so now…
Tell us what you're selling.
Send us your store. Within one business day you get a short Loom from a senior: the three things we'd fix first, what it would cost, and whether we're the right team for it.
- No pitch deck, no discovery-call theatre
- You keep the audit whether or not you hire us
- Fixed-scope quotes, no hourly surprises
Prefer to talk? Book 20 minutes with Haniel or call +1 855-764-4977