Best High Risk Payment Gateways for Shopify Stores

Introduction

Operating in a high-risk industry should not prevent you from using the world’s most powerful e-commerce platform. While Shopify Payments is the default choice for many, its strict underwriting guidelines often exclude merchants selling products like CBD, supplements, or high-ticket electronics. When these merchants are flagged, they often face frozen funds or sudden account termination. Finding a reliable third-party processor is the only way to maintain a stable revenue stream.

We developed HidePay on the Shopify App Store to give merchants the tools they need to manage these alternative payment methods effectively. Whether you are navigating regional regulations or trying to reduce chargeback ratios, controlling how and when your payment options appear is vital. This article covers how to identify the right high-risk gateway, the steps to integrate one with your store, and how to optimize your checkout to protect your business.

By the end of this guide, you will understand how to secure a high-risk merchant account and use sophisticated rules to manage your checkout experience.

Understanding High Risk in the Shopify Ecosystem

The term "high risk" is often misunderstood by newer merchants. It does not necessarily mean your business is doing something wrong or illegal. Instead, it refers to the level of financial risk a payment processor assumes when handling your transactions. Shopify Payments, which is powered by Stripe, is designed for low-risk, predictable retail models. If your business deviates from that model, you are likely to be categorized as high risk.

There are two primary reasons why a store falls into this category. The first is the industry itself. Products with complex regulations, such as tobacco, firearms, or nutraceuticals, are automatically flagged. The second reason is your operational history. If your store has a chargeback rate exceeding 1%, or if you deal in high-ticket items with long shipping delays—common in dropshipping—processors view you as a liability.

When Shopify Payments identifies a high-risk merchant, they typically pause payouts first to conduct an audit. If they determine the risk is too high, they will disable the gateway entirely. This is why many experienced merchants in these sectors choose to use a dedicated third-party gateway from the start. It provides a level of stability that "one-size-fits-all" aggregators cannot offer.

The Difference Between a Gateway and a Merchant Account

Before selecting a provider, you must understand the two distinct components required to process high-risk payments. Many merchants use these terms interchangeably, but they serve very different roles.

The Payment Gateway

The gateway is the software layer that connects your Shopify checkout to the processing network. It encrypts the customer’s credit card data and sends it to the processor for approval. For high-risk merchants, the most common gateways are Authorize.net and NMI (Network Merchants Inc.). These platforms are highly flexible and allow you to connect multiple merchant accounts to a single checkout.

The Merchant Account

The merchant account is the actual bank account where funds are held before being deposited into your business checking account. High-risk merchant accounts are underwritten by banks that specialize in "hard-to-place" businesses. These banks are comfortable with higher chargeback volumes because they charge higher processing fees and may implement a "reserve"—a percentage of your sales held back to cover potential disputes.

To operate successfully on Shopify, you generally need both. You apply for a merchant account through a high-risk specialist, and they provide you with the credentials to a compatible gateway.

Top High-Risk Payment Gateways for Shopify

Choosing a provider depends on your specific product category and where your customers are located. Because Shopify is a global platform, we recommend looking for providers that offer international support and multi-currency processing.

1. Authorize.net

Authorize.net is perhaps the most well-known gateway for Shopify users. It is a veteran in the space and has a direct integration with Shopify’s "Alternative Payment Provider" settings. While Authorize.net itself has an internal payment service that is low-risk, the gateway software can be used to connect to almost any high-risk merchant account. This makes it a versatile choice for stores that need a reliable, professional checkout.

2. NMI (Network Merchants Inc.)

NMI is a favorite for high-volume merchants because of a feature called "Load Balancing." This allows you to connect multiple merchant accounts to the same gateway. If one account reaches its monthly processing limit or sees a spike in chargebacks, the gateway automatically routes transactions to a different account. This prevents your entire store from going dark if one bank decides to pause your service.

3. Bankful

Bankful has gained popularity specifically for industries like CBD and subscriptions. They offer a native Shopify integration and are known for a faster approval process than traditional banks. They also provide tools for managing recurring billing, which is often a pain point for high-risk stores.

4. DigiPay and PaymentCloud

These are not just gateways; they are full-service merchant service providers. They work with a network of banks to find a home for your business regardless of your industry. They then provide the gateway technology (often a white-labeled version of NMI or Authorize.net) to plug directly into your Shopify admin.

How to Set Up a Third-Party Gateway on Shopify

Once you have been approved for a high-risk merchant account, the integration process is straightforward. However, you must follow the steps precisely to avoid checkout errors that can lead to abandoned carts.

1. Access Payment Settings: In your Shopify admin, navigate to the Settings menu and select "Payments."
2. Choose a Provider: If you have Shopify Payments active, you may need to click "Manage" and then "Switch to a third-party provider." If you have never set up payments, look for "Choose a provider" under the third-party providers section.
3. Enter Credentials: Select your gateway (e.g., Authorize.net) from the list. You will be prompted to enter your API Login ID and Transaction Key. These are provided by your merchant account representative, not by Shopify.
4. Disable Duplicate Emails: Many third-party gateways are configured to send their own transaction receipts by default. Since Shopify already sends a professional order confirmation email, you should log into your gateway's dashboard and disable "Merchant Email Receipts" to avoid confusing your customers.
5. Test the Integration: Always perform a test transaction using a real credit card. Verify that the order appears in your Shopify admin and that the funds show as "Pending" or "Captured" in your gateway dashboard.

Optimizing Your Checkout with HidePay

Adding a high-risk gateway is only the first step. To truly protect your margins and improve conversion rates, you need granular control over when these payment methods are visible. Shopify’s default settings are often too broad; they either show a payment method to everyone or no one.

This is where the "Smart Checkout" approach becomes essential. Using install HidePay, you can create specific rules that show or hide payment methods based on the contents of the cart or the customer’s location.

Rule-Based Visibility

Not every product in your store may be high-risk. If you sell both apparel and CBD products, you might want to use a standard processor for the clothing to save on fees and reserve the high-risk gateway only for orders containing CBD. Our app allows you to trigger payment options based on product tags or collections—see the guide on How to create a payment customization to get started. This ensures you are not paying high-risk processing rates on low-risk transactions.

Geographic Controls

Some high-risk gateways only support specific currencies or countries. If you use a provider that only accepts USD, there is no reason to show that option to a customer in the UK who wants to pay in GBP. By setting a geography-based rule, you ensure that customers only see payment methods they can actually use. This reduces friction and prevents "payment failed" errors at the final stage of checkout—learn about country and market settings in the HidePay docs.

Sorting for Better Conversions

The order in which payment methods appear significantly impacts which one a customer chooses. If you have a preferred gateway with lower fees or a more reliable approval rate, you should move it to the top of the list. Follow the step‑by‑step instructions in Sort and Rename payment methods in the Checkout to reorder and rename options for clearer billing descriptors and better conversions.

Managing Chargebacks and Protecting Your Account

For a high-risk merchant, a chargeback is more than just a lost sale; it is a threat to your ability to process payments. If your chargeback rate stays high for too long, your bank will close your account and report you to the MATCH list (Member Alert to Control High-risk merchants), making it nearly impossible to get another account for years.

To prevent this, you must be proactive.

• Clear Billing Descriptors: Ensure the name that appears on the customer’s bank statement matches your store name. If a customer sees a charge from "Nextools Limited" but they bought from "SuperSupplements.com," they might file a fraud claim out of confusion.
• Prioritize Support: Make your contact information highly visible. It is better for a customer to ask you for a refund than to call their bank for a chargeback.
• Use Fraud Prevention Tools: Most high-risk gateways include an Advanced Fraud Suite. Enable features like Address Verification (AVS) and Card Code Verification (CVV). These simple checks stop a large percentage of fraudulent transactions before they are even processed.
• Strategic Hiding: If you notice a specific region or customer group has a high fraud rate, use a rule to hide credit card options for those segments and offer only non-reversible methods, or hide the high-risk gateway entirely for those specific orders.

If you need detailed troubleshooting, the HidePay help center includes articles such as How to Retrieve the Correct Payment Method in HidePay and How to share Debug Logs in HidePay to speed up diagnosis.

The Technical Edge: Why Native Shopify Functions Matter

In the past, merchants had to rely on Shopify Scripts to modify their checkout. This required a Shopify Plus subscription and complex coding knowledge. Because Scripts are being deprecated, modern merchants need a more reliable solution.

The app is built on Native Shopify Functions. This is a technical distinction that matters for two reasons: speed and security. Because the logic runs natively within Shopify's infrastructure, there is zero latency. Your checkout remains fast, which is critical for conversion. Furthermore, because it does not rely on external scripts or "hacks," it is fully compatible with the latest Shopify checkout updates and mobile optimizations.

If you want a short primer on why functions replace scripts, read Nextools’ explainer in the post about Why Shopify Functions are the future. For a product-focused overview, the Nextools article Introducing HidePay for Shopify, say goodbye to irrelevant payment options and high cost walks through common merchant use cases and the technical benefits.

Navigating the Transition After a Ban

If you are reading this because Shopify Payments has already suspended your account, the priority is to keep your store active while you wait for a new gateway.

First, do not delete your Shopify store. A payment suspension is rarely a full platform ban. You can still accept orders through alternative methods like PayPal or manual bank transfers in the interim.

Second, apply for a high-risk account immediately. The underwriting process for these accounts can take anywhere from three days to two weeks. You will need to provide business registration documents, bank statements, and a valid ID. Be transparent with your new processor about why your previous account was closed; they are experts at handling these situations and can often structure your new account to avoid the same pitfalls.

Finally, once your new gateway is active, use a tool like ours to slowly ramp up your volume. Start by showing the new gateway only to a small segment of customers to ensure the integration is stable before opening it up to your entire audience.

Conclusion

Securing a high-risk payment gateway is a necessary step for any Shopify merchant operating in a regulated or high-dispute industry. While it involves higher fees and more paperwork than Shopify Payments, the stability it provides is invaluable for long-term growth. By selecting the right provider—such as Authorize.net or NMI—and connecting it to a specialized merchant account, you can protect your business from sudden cash flow interruptions.

Success in high-risk e-commerce requires more than just a gateway; it requires control over your checkout environment.

• Identify the specific risk factors for your industry.
• Select a gateway that supports your products and geographic markets.
• Use sophisticated rules to hide or sort payment methods based on cart data.
• Monitor your chargeback rates and adjust your visibility rules accordingly.

If you are ready to take full control of your checkout and optimize your payment strategy, you can try HidePay on Shopify to begin building your custom rules today. To explore other Nextools tools that work well with HidePay, see the Nextools app suite.

FAQ

Is it legal to use high-risk payment gateways on Shopify?

Yes, it is completely legal. Shopify explicitly allows the use of third-party payment providers. In fact, they provide a directory of compatible gateways precisely so that merchants in industries not supported by Shopify Payments can still run their businesses on the platform. For setup details, consult the HidePay documentation in the Help Center.

Why does Shopify charge an extra fee for third-party gateways?

Shopify charges a transaction fee (ranging from 0.5% to 2%, depending on your plan) when you use a third-party processor. This is because they are not earning the processing fee they would normally get through Shopify Payments. For many high-risk merchants, this small extra cost is worth the added security of a stable, dedicated processor.

Can I use multiple high-risk gateways at the same time?

Technically, Shopify allows you to have one primary credit card processor and several alternative methods (like PayPal or Alternative Payment Providers). If you need to use multiple credit card gateways, you typically use a gateway like NMI that can manage multiple merchant accounts behind the scenes.

Will using a high-risk gateway slow down my checkout?

Not if you use modern tools. If your payment rules are handled through native infrastructure, like the Shopify Functions used by HidePay, there is no impact on page load times. The customer experience remains as fast as a standard Shopify checkout.

How do I hide PayPal or Express checkout buttons?

HidePay supports hiding Express Checkout buttons and PayPal in specific scenarios; see the help article Hide PayPal Express Checkout Button in checkout for step‑by‑step instructions and limitations.

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Ready to get started? Visit the HidePay listing on the Shopify App Store to get HidePay for your store and start creating payment customizations today.