Adding a payment method you've built yourself to Shopify's checkout isn't something every store can do. As a rule, only payment providers approved by Shopify can build the payment apps that run on Shopify's checkout. The one exception is that eligible Shopify Plus stores can build a custom payments extension that works only on their own store. For other stores, a "custom payment setup" usually means using an approved provider's app, customising payment methods with Shopify Functions, or taking payment outside Shopify and creating the order via the API.
In this article we explain when each of these routes is suitable, the custom payments extension option for Shopify Plus stores and how to integrate with Shopify as a payment company.
How does payment infrastructure work on Shopify?
On Shopify, customers always pay on Shopify's checkout. The payment methods shown there come from three sources:
Shopify Payments: Shopify's own infrastructure. Not available in Turkey.
Third-party payment provider apps: apps from providers approved by Shopify, such as iyzico and PayTR.
Manual payment methods: methods such as bank transfer and cash on delivery, where payment is taken outside Shopify.
This structure exists for security and PCI DSS compliance: card details are processed only by approved and audited providers.
Route 1: Using an approved payment provider
For most stores, the right solution is to install the app of an approved payment provider that meets their needs. Providers in Turkey cover needs such as instalments, 3D Secure and local cards. Setup usually takes a few hours, and maintenance is the provider's responsibility.
We cover the status of Shopify Payments in Turkey and provider options in our Shopify Payments article, and iyzico setup in our iyzico integration article.
Route 2: Customising payment methods with Shopify Functions
If you want to control which payment method is shown to which customer without changing the existing methods, Shopify Functions' payment customisation feature helps:
Hiding cash on delivery for orders above a certain amount
Showing only bank transfer to B2B customers
Reordering payment methods by country
Renaming a payment method
These customisations can be done on all plans with ready-made apps from the App Store. Using Functions with apps built specifically for your store requires Shopify Plus. This route doesn't add a new payment method; it changes how existing methods behave.
Route 3: Taking payment outside Shopify and creating the order via the API
In some business models, payment is taken in another system rather than on Shopify's checkout:
Recurring payments through a payment provider's own subscription infrastructure
Current accounts, cheques or deferred payment for dealers or B2B customers
Payment links sent to customers by sales representatives
In this case, a custom app creates the order in Shopify via the Admin API and marks it as paid once payment succeeds. That way stock, order management, shipping and accounting integrations keep working through Shopify. We discuss this approach for subscriptions in our Shopify Subscriptions article.
Things to watch with this route:
As payment doesn't happen on Shopify's checkout, Shopify's fraud analysis and payment reports don't cover these orders.
Refunds and cancellations need to be managed separately on the payment provider's side.
Card details must never pass through your own server; use the payment provider's hosted payment page or secure form.
Route 4: Custom payments extensions for Shopify Plus stores
Shopify allows eligible Shopify Plus stores to build a custom payments extension that runs only on their own store. This lets you offer, for example, the virtual POS of a bank you have a direct agreement with, or a payment provider without a ready-made Shopify app, as a native payment method on Shopify's checkout.
The conditions for this route:
Eligibility depends on Shopify's approval. Before you start, you need to talk to Shopify Plus Support and confirm your store is eligible for this option.
The extension is built with Shopify's Payments Apps API and payments extension framework; requirements such as processing card data in secure fields, 3D Secure support and PCI DSS apply.
The extension works only on your store and isn't listed in the App Store.
Development and maintenance are your responsibility or your agency's. Shopify API version updates need to be tracked.
For large brands that want to use a custom payment setup while keeping the payment experience on Shopify's checkout, this option is the cleanest solution.
For payment companies: integrating with Shopify as a payment provider
If you're a payment institution and want to serve Shopify stores, you need to apply to Shopify's payments partner programme. The process generally consists of these steps:
Open a Shopify Partner account and apply for the payments partnership.
Pass Shopify's review: company details, licences, PCI DSS compliance and risk management processes are assessed.
Build a payments app with the Payments Apps API: choose the appropriate type from card, alternative or redirect payments.
Testing and app review: the app is tested against Shopify's technical and user experience requirements.
Launch: the approved app is listed as a payment provider stores can install.
This process can take months and isn't a route a store would follow on its own.
Which route suits you?
Need | Recommended route |
|---|---|
Card payments, instalments, 3D Secure | An approved payment provider's app |
Offering your agreed bank's virtual POS as a native method on checkout (Shopify Plus) | Shopify Plus custom payments extension |
Hiding or reordering payment methods by customer | Payment customisation with Shopify Functions |
Subscriptions, current accounts or deferred payment | A custom app that takes payment externally and creates the order via the API |
Being listed on Shopify as a payment company | Shopify's payments partner programme |
Frequently asked questions
Can I add my own payment system to Shopify checkout?
If you use Shopify Plus and Shopify finds you eligible, you can build a custom payments extension for your store. You need to confirm eligibility with Shopify Plus Support. On other plans, stores use approved providers' apps or take payment outside Shopify and create the order via the API.
Do I need Shopify Plus for a custom payment integration?
You don't need it to use an approved payment provider. Building a custom payments extension for your store, and customising payment methods with Shopify Functions using store-specific apps, do require Shopify Plus.
How do I add bank transfer or cash on delivery?
You can add them from the manual payment methods section on the Settings → Payments page in your Shopify admin. With these methods, you confirm that payment has been received.
Let's plan your payment setup together
The right payment setup directly affects both your conversion rate and your operational workload. If you'd like to plan the best payment infrastructure or a custom integration for your store together, get in touch through our Shopify technical support page.
