How to Add a Custom Payment Method in Shopify

Introduction

Providing the right payment options at checkout is a direct lever for increasing conversion rates and reducing cart abandonment. While Shopify offers integrated solutions like Shopify Payments and dozens of third-party gateways, many merchants eventually need to offer something more specific to their business model. Whether you are handling wholesale orders, offering local cash-on-delivery, or requiring bank transfers for high-ticket items, knowing how to add and manage custom payment methods is essential for growth.

We built HidePay to give merchants the granular control they need over these options once they are added to the store. See HidePay on the Shopify App Store. This guide explains the technical steps to add custom and manual payment methods and, more importantly, how to manage them strategically so they only appear to the right customers at the right time. You will learn how to move beyond basic settings to create a checkout experience that protects your margins and serves your global audience.

By the end of this article, you will understand the difference between integrated providers and manual methods, how to set them up in your admin, and how to use logic-based rules to ensure your checkout remains clean and professional. For background on the app and its launch, see Introducing HidePay for Shopify.

Understanding Shopify Payment Categories

Before adding a new method, you must distinguish between the two primary ways Shopify handles transactions. Most merchants use a combination of both to satisfy different customer segments.

Integrated Third-Party Providers

These are payment gateways like Stripe, Authorize.net, or region-specific providers like Mollie or Paystack. These services handle the transaction processing, security, and PCI compliance on their own servers. When a customer pays via an integrated provider, the funds are automatically captured (or authorized) and eventually transferred to your merchant account. Adding these usually involves "installing" the provider's app from the Shopify App Store or entering API credentials in your payment settings.

Manual Payment Methods

Manual methods are used for transactions that happen outside of the Shopify online checkout flow. When a customer chooses a manual method, the order is marked as "Pending" in your admin. You are responsible for collecting the payment and then manually marking the order as paid. Common examples include:

• Bank Deposits: Providing your IBAN or account details for wire transfers.
• Cash on Delivery (COD): Collecting payment when the courier delivers the goods.
• Money Orders: Traditional paper-based payments.
• Custom Manual Methods: Anything else you define, such as "Net 30" for B2B clients or "Pay in Store" for local pickup.

For the purpose of "adding a custom method," most merchants are looking for the Manual Payment option. This is the most flexible way to introduce a non-standard payment type without needing deep technical integrations.

How to Add a Manual Custom Payment Method

Adding a manual method is a straightforward process within your Shopify admin. This allows you to create a labeled option that appears alongside credit card and express checkout buttons.

1. Navigate to your Settings and select Payments.
2. Scroll down to the Manual payment methods section.
3. Click the Add manual payment method dropdown.
4. Choose a preset (like Bank Deposit) or select Create custom payment method.
5. Enter a name for the method. This name is what the customer will see at checkout.
6. Provide Additional details. Use this space to explain how the payment works (e.g., "Your order will ship once the wire transfer is confirmed").
7. Add Payment instructions. These appear on the order confirmation page and in the confirmation email.

While this adds the method to your store, Shopify’s default behavior is to show this method to every customer, regardless of their location, what they are buying, or who they are. This is where most merchants run into friction, as showing a "Bank Transfer" option to a retail customer buying a $10 item can look unprofessional or cause confusion.

Why Standard Setup Often Falls Short

The challenge for a growing store is not just adding the method, but controlling its visibility. If you add "Wholesale - Net 30" as a custom manual method, you likely only want your tagged B2B customers to see it. If it is visible to everyone, retail customers might select it to bypass paying upfront, leading to a backlog of unpaid orders and a heavy administrative burden for your team.

Similarly, Cash on Delivery is highly effective in certain regions but carries a high risk of "Return to Sender" (RTS) in others. If you offer COD globally, your shipping costs and failed delivery rates will skyrocket. The standard Shopify admin does not allow you to hide these manual methods based on the customer's country or the contents of their cart.

To solve this, we utilize Shopify Functions. This technology allows us to intercept the checkout process and apply logic to the payment methods. Instead of a static list of options, your checkout becomes dynamic.

Using Logic to Control Custom Payment Visibility

Once you have added your custom methods, the next step is defining the rules for when they should appear. Effective management involves filtering out irrelevant options to reduce "choice paralysis" for the customer. For a step‑by‑step on creating rules inside the app, see How to create a payment customization.

Geography-Based Rules

If you offer a custom payment method specifically for your home country, such as a local bank transfer, you should hide that method for all international visitors. This keeps the checkout clean for global customers who would find the option irrelevant.

• Action: Create a rule that hides the custom manual method if the shipping country is not your local market.
• Result: Only customers in the target region see the specialized payment option. For a guided example that hides Cash on Delivery for foreign customers, see How to Hide Cash on Delivery for Foreign Customers with HidePay.

Cart Total and Currency Rules

Manual payments like bank transfers are often preferred for high-value orders to avoid the high percentage fees associated with credit card processors. Conversely, you might want to disable certain "Buy Now, Pay Later" (BNPL) options for very small orders where the fixed transaction fees eat too much into your margin.

• Action: Set a minimum cart total for your "Bank Wire" option.
• Result: The option only appears when the order value justifies the manual processing time.

Customer Tag Segmentation

This is the most common use case for B2B and wholesale operations. If you have a group of trusted distributors, you can tag them as "Wholesale" in your Shopify admin.

• Action: Hide the "Net 30" or "Invoice" payment method for any customer who does not have the "Wholesale" tag.
• Result: Regular retail customers only see standard payment options, while your professional partners see their negotiated terms.

Sorting and Renaming for Better Conversion

Adding a custom method is only half the battle; how that method is presented matters just as much. The order in which payment options appear can influence which one a customer chooses.

Sorting Strategies

By default, Shopify often prioritizes its own integrated methods or lists them alphabetically. However, you may want to guide customers toward the method that is most cost-effective for you or most convenient for them. Within HidePay, you can reorder the list to ensure your preferred provider is at the top.

For example, if you have recently added a custom payment method for a local gateway that has lower transaction fees, you can move it to the first position. By making it the path of least resistance, you can significantly impact your monthly processing costs.

The Power of Renaming

The "Additional details" field in Shopify is useful, but the title of the payment method is what catches the eye first. Sometimes, the default name of a provider or a manual method doesn't quite fit your brand voice or the customer's expectations in a specific region.

You can rename any payment method dynamically. If "Manual Bank Deposit" sounds too clinical, you might rename it to "Secure Bank Transfer" or "Pay via [Your Bank Name]." For international stores, renaming methods into the local language based on the customer’s currency or country is a powerful way to build trust during the final steps of the purchase.

Blocking Express Checkout Buttons

When you add custom payment methods, they appear in the final "Payment" step of the checkout. However, many customers use "Express Checkout" buttons (like Apple Pay, Google Pay, or PayPal Express) found on the first page of the checkout or even on the product page.

If your goal is to funnel customers toward a specific custom method—perhaps because you need to collect specific order attributes or because you're selling a product category that those express providers don't allow—you may need to hide these buttons. We provide the ability to block these express buttons based on the same rules you use for hiding payment methods. If a customer has a specific product in their cart that violates a provider's terms of service, you can hide that provider's button entirely to prevent a failed transaction later in the process. For instructions on disabling express checkout buttons, see Hide the Express Checkout with HidePay.

Key Scenarios for Custom Payment Logic

To help you decide which rules to implement, consider these practical merchant scenarios. Each of these can be handled through the tool we’ve developed.

The High-Risk Product Scenario

If you sell products that are frequently flagged for chargebacks, you might want to disable credit card payments for those specific items and only allow manual bank transfers.

1. Identify the high-risk products by tag or SKU.
2. Create a rule to hide credit card gateways when those products are in the cart.
3. Show your custom "Bank Transfer" method instead. If you need to block certain orders entirely at checkout (for fraud or validation rules), an order‑validation app like CartBlock on the Shopify App Store can help enforce additional checks before payment.

The B2B / Wholesale Hybrid Store

Many merchants run one store for both retail and wholesale.

1. Add a manual method called "Pay by Invoice."
2. Create a rule that hides this method unless the customer is logged in and tagged as "B2B."
3. This prevents retail customers from selecting an option that requires manual invoicing.

The Regional COD Strategy

Cash on Delivery is essential in markets like India, Southeast Asia, or parts of the Middle East, but risky elsewhere.

1. Enable the manual "Cash on Delivery" method in Shopify.
2. Create a rule to hide COD for all countries except your target regions.
3. Add a further rule to hide COD if the order value exceeds a certain amount, reducing the risk of high-value non-deliveries. For complementary shipping logic (e.g., hiding specific shipping methods in the same regions), consider HideShip on the Shopify App Store.

Setting Up Your Rules: A Step-by-Step Approach

When you are ready to move beyond basic manual methods, follow this workflow to ensure your checkout remains optimized.

1. Audit your current methods: Look at your Shopify payment settings. Are there methods you currently offer that have high fees or high chargeback rates?
2. Define your segments: Decide which customers should see which methods. Consider geography, order value, and customer loyalty.
3. Install the right tool: Use an app like install HidePay that uses Shopify Functions. This ensures the logic runs natively within Shopify's infrastructure, providing the fastest possible checkout experience for your customers.
4. Create your first rule: Start simple. Choose one method and one condition (e.g., hide a specific method for a specific country).
5. Test the checkout: Use Shopify’s "Preview" mode or place test orders from different locations (using a VPN if necessary) to ensure the logic is firing correctly.
6. Refine and stack: Once your first rule is working, you can add more complex logic, such as rules based on cart contents or delivery methods.

Technical Foundations: Shopify Functions

It is important to understand why we use Shopify Functions for these customizations. In the past, merchants on Shopify Plus used "Shopify Scripts" to modify the checkout. This required knowledge of the Ruby programming language and was only available to high-enterprise stores.

Today, Shopify Functions has replaced scripts and made this level of customization available to all plans (though some specific checkout extensibility features may vary by Shopify plan). Because HidePay is built on these native functions, it does not rely on "hacks" or theme code edits. This means:

• Performance: There is no delay in loading the checkout. The logic happens instantly.
• Reliability: Since it is a native part of the Shopify checkout flow, it is less likely to break when Shopify updates its platform.
• Security: Your customer's sensitive payment data never leaves Shopify's secure environment.

If you need tools to migrate legacy Scripts or generate Functions without coding, see SupaEasy on the Shopify App Store. For additional context about the move from Scripts to Functions, read our post "Shopify Script Editor no longer available: say Adios to Scripts and Hello to Functions!" (Nextools Tech).

Summary of Action Steps

If you are ready to customize your checkout today, here is the most efficient path forward:

• Add your manual methods: Go to Settings > Payments and create the custom options you need.
• Install a management tool: Download the app from the Shopify App Store to start creating rules.
• Organize your options: Use the "Sort" feature to put your most profitable or highest-converting methods at the top of the list.
• Protect your margins: Use "Hide" rules to remove risky or high-fee options for specific products or regions.
• Monitor and adjust: Check your conversion rates. If a specific manual method is causing a lot of pending orders that never get paid, consider adding a "minimum cart total" rule to that method.

If you want a single billing option that bundles payment and shipping controls, read about HideSuite — it combines HidePay and HideShip into a single suite for merchants who need both payment and shipping rules.

Conclusion

Adding a custom payment method is a vital step for any merchant looking to escape the "one-size-fits-all" approach of standard e-commerce. By combining Shopify’s manual payment settings with the logic-based control of HidePay, you can create a checkout that feels local to every customer while protecting your business from unnecessary fees and risks.

Whether you need to hide certain options for specific countries, sort your list to highlight preferred gateways, or rename methods for better clarity, the tools are now available to do so without touching a single line of code. We invite you to explore these features and see how a cleaner, more relevant checkout can improve your bottom line.

To get started with advanced payment rules, you can view the app and check current pricing on the Shopify App Store.

FAQ

Can I add a custom credit card processor to Shopify?

You cannot easily add a completely new, unlisted credit card processor yourself because Shopify requires gateways to be integrated via their official Payment Provider API. However, you can add any "Manual" payment method (like Bank Transfer or COD) and give it a custom name. For standard credit card processing, you must choose from the hundreds of providers already supported by Shopify in your region.

How do I show a payment method only for B2B customers?

To show a payment method exclusively for B2B customers, you first add it as a manual payment method in your Shopify settings. Then, you use an app like our tool to create a "Hide" rule. You set the condition to hide that specific payment method for any customer who does not have a specific tag, such as "Wholesale" or "B2B," in their customer profile.

Is it possible to hide PayPal for certain products?

Yes, you can hide PayPal or any other payment method based on the products in the customer's cart. Within the app, you create a rule that identifies specific product tags, SKUs, or collections. When those items are detected in the cart, the app uses Shopify Functions to remove the PayPal option from the list of available payments at checkout.

Does adding custom payment rules slow down my checkout?

When you use a tool built on Native Shopify Functions, like our app, there is no noticeable impact on checkout speed. Unlike older methods that used theme scripts or external workarounds, Shopify Functions run directly on Shopify's servers during the checkout process. This ensures that your payment methods are filtered and sorted instantly as the page loads.

Where can I add more checkout controls, validations, or advanced functions?

If you need extra checkout validations (block or validate orders before payment) consider CartBlock on the Shopify App Store for order validation, or explore SupaEasy on the Shopify App Store to generate and migrate Shopify Functions. If you need to manage shipping visibility alongside payments, see HideShip on the Shopify App Store.