Introduction
You do not need a standalone Stripe account to run a Shopify store because the platform provides its own integrated solution called Shopify Payments. This built-in system is actually powered by Stripe’s infrastructure, meaning you get the reliability of their technology without needing to manage a separate third-party account. Choosing between the two often comes down to your location, your business model, and how much control you want over your checkout experience.
We see many merchants struggle with this decision when first launching their stores. While the integration between these two companies is deep, the way they affect your daily operations and transaction fees differs significantly. Using a tool like HidePay on the Shopify App Store allows you to manage these options effectively, but the foundation starts with understanding which gateway is the right fit for your specific market.
This article clarifies the relationship between Stripe and Shopify, explains when a dedicated Stripe account is necessary, and outlines the cost implications of each choice. By the end, you will know exactly which payment setup serves your business goals.
The Relationship Between Shopify and Stripe
It is a common point of confusion for new merchants to realize that Shopify and Stripe are partners rather than direct competitors. Shopify Payments is a white-label version of Stripe. This means when you use the default payment setting in your Shopify admin, you are using Stripe’s processing engine under the hood.
Because of this partnership, you get the benefits of Stripe’s global financial network—high uptime, secure encryption, and fast processing—directly within your Shopify dashboard. You do not have to log into a separate website to see your payouts or manage disputes. Everything is centralized, which simplifies your bookkeeping and daily management.
However, a standalone Stripe account is a different product. It is a highly customizable "developer-first" platform. While Shopify Payments is built for ease of use within a specific ecosystem, Stripe is built to be integrated into any website or custom application. For most standard e-commerce stores, the integrated version is sufficient, but there are specific scenarios where the standalone version becomes a requirement.
When You Must Use a Standalone Stripe Account
While Shopify Payments is the preferred option for many, it is not available to everyone. You will need to set up a standalone Stripe account (or another third-party gateway) if you fall into one of the following categories.
1. Geographic Restrictions
Shopify Payments is currently available in approximately 23 countries, including the United States, United Kingdom, Canada, Australia, and several European nations. If your business is registered in a country not on this list—such as Brazil, India, or Mexico—you cannot use the integrated solution. In these regions, Stripe is often the most reliable alternative, provided they support your specific country.
2. High-Risk Business Categories
Every payment processor has a Terms of Service agreement that lists "prohibited businesses." Because Shopify Payments is a simplified version of the service, its risk filters can sometimes be more rigid than Stripe’s standalone platform. If you sell products that fall into "grey area" categories, you might find that Shopify Payments declines your application while a custom-configured Stripe account, which allows for more detailed risk underwriting, might accept you.
3. Advanced Technical Requirements
If you are running a complex B2B operation or a custom-coded storefront that exists outside of the standard Shopify Online Store framework, you might need the direct API access that a standalone Stripe account provides. Most merchants using the standard Shopify themes and checkout do not need this level of technical depth.
Hide, sort, and rename Shopify payment methods using powerful conditions. Customize your checkout and control payment options with HidePay.
Understanding the "Third-Party Transaction Fee"
The most significant reason to stick with Shopify Payments rather than a standalone Stripe account is the cost. Shopify incentivizes merchants to use their internal gateway by waiving third-party transaction fees.
If you choose to use an external Stripe account, Shopify will charge you an additional fee on every order. This fee varies depending on your Shopify plan:
- Basic Plan: 2.0% extra per transaction
- Shopify Plan: 1.0% extra per transaction
- Advanced Plan: 0.5% extra per transaction
These percentages are on top of the processing fees Stripe already charges you (typically 2.9% + $0.30). By using the integrated Shopify Payments, you completely eliminate these extra 0.5% to 2.0% charges. For a growing business, this difference can represent thousands of dollars in annual profit.
Comparing Features: Stripe vs. Shopify Payments
Even though they share the same DNA, the two options offer different tools for managing your money.
Integration and Setup
Shopify Payments is active the moment you start your store. You simply enter your bank details and business information. A standalone Stripe account requires you to create the account on Stripe’s website, verify your identity there, and then copy API keys or connection settings back into your Shopify admin.
Payout Speed
Both services generally offer a 2-to-3 business day payout schedule, depending on your region. However, Shopify Payments users often have access to "Shopify Balance," a business account that can receive payouts faster—sometimes within one business day.
Subscription Management
If you sell recurring subscriptions, Stripe has a very powerful native billing engine. While Shopify has made great strides in subscription support, many merchants still prefer Stripe’s "Billing" product for complex recurring models. That said, most Shopify merchants use apps from the Shopify App Store to handle subscriptions, which work perfectly with both gateways.
Data and Reporting
Stripe provides incredibly deep data visualizations and SQL-based reporting through a tool called Stripe Sigma. Shopify provides excellent sales reports that are easier for non-technical users to read. If you have a dedicated data analyst on your team, they will likely prefer Stripe’s raw data access. If you are a solo founder, Shopify’s built-in reports are usually more than enough.
Optimizing the Checkout Experience
Regardless of whether you use Stripe or Shopify Payments, your goal is to make the checkout process as frictionless as possible. Offering too many payment methods can actually hurt your conversion rate by overwhelming the customer. Conversely, hiding the preferred local payment method in a specific country can lead to cart abandonment.
Our app, HidePay, gives you the control to decide exactly when and where specific payment methods appear. For example, if you use a third-party gateway like Stripe alongside PayPal and a "Buy Now, Pay Later" (BNPL) option, your checkout can start to look cluttered.
We designed the app to allow merchants to:
- Sort payment methods: Move your most cost-effective gateway (like Shopify Payments) to the top of the list. See the guide on Sort and Rename payment methods in the Checkout to learn how to reorder and rename methods.
- Hide methods by country: If Stripe is your primary gateway but you know a specific region prefers a local bank transfer, you can hide the credit card option or reorder it; follow How to easily organize payment methods by country or by Shopify Market for step-by-step instructions.
- Rename options: You can change "Stripe" or "Credit Card" to something more recognizable to your specific audience — see How to create a payment customization for renaming and other rule setup details.
If you also need to control which shipping options appear (to avoid unexpected carrier fees or mis-selected rates), consider pairing payment rules with our shipping app: HideShip on the Shopify App Store.
By using these rules, you ensure that the customer only sees the most relevant, high-converting options. This reduces "analysis paralysis" at the final stage of the purchase.
Practical Scenarios: Which Should You Choose?
To help you decide, consider these common merchant situations:
The New Merchant (US, UK, or Canada)
If you are just starting and live in a supported country, use Shopify Payments. It is the most cost-effective choice because it avoids the third-party transaction fee. It is also the easiest to manage since your financial data stays inside the Shopify admin.
The International Merchant (Unsupported Regions)
If you are based in a country like Singapore or Italy where Shopify Payments is available, use it. If you are in a country where it is not available, a standalone Stripe account is your best bet. Even with the extra transaction fee from Shopify, Stripe’s reliability and global reach make it a superior choice to many local, smaller gateways.
The B2B or High-Ticket Merchant
If you sell expensive items (over $5,000), you may want to use a standalone Stripe account to take advantage of their lower ACH (bank transfer) fees. Stripe charges a capped fee for ACH, whereas credit card percentages can become massive on high-ticket items. In this case, the 0.5%–2% penalty from Shopify might be smaller than the savings you get from using ACH through Stripe.
What to do next:
- Check the "Payments" section in your Shopify admin to see if Shopify Payments is available in your region.
- Compare your projected monthly volume against the third-party fee to see if an external gateway is worth the cost.
- Consider how many payment options you currently show at checkout and if they are helping or hurting your conversion rate. If you need help identifying the exact payment method names shown in your checkout for rule setup, see How to Retrieve the Correct Payment Method in HidePay.
Why Native Shopify Functions Matter
When you choose a tool to manage your checkout, it is important to understand how it interacts with Shopify's code. Older apps used "hacks" or theme code edits to hide or reorder payment methods. These were often slow and could break during high-traffic events like Black Friday.
The tool we built at Nextools is based on Native Shopify Functions. This means it runs directly on Shopify’s servers, not as a script on your storefront. This ensures that your checkout remains fast and secure, regardless of how many rules you set up to hide or sort your Stripe or Shopify Payments options. To understand why Functions are the future of checkout customization, read our post: Why Shopify Functions are the future and scripts are the past. This "Built for Shopify" approach is the current gold standard for platform stability.
Conclusion
You do not need a separate Stripe account to succeed on Shopify. For the vast majority of merchants, Shopify Payments provides the best balance of low fees, easy setup, and integrated reporting. You only need a standalone Stripe account if you are in an unsupported country, a high-risk industry, or have very specific technical needs that require direct API access.
Optimizing your checkout is about more than just choosing a provider; it is about presenting the right options at the right time. Our app, HidePay, helps you refine that experience by giving you total control over how those payment methods appear to your customers. By reducing clutter and highlighting the most trusted local options, you can protect your margins and improve your conversion rates.
Ready to take control of your checkout? You can install HidePay and start creating a cleaner, more efficient payment experience for your customers.
FAQ
Does Shopify use Stripe?
Yes, Shopify Payments is built on Stripe's technology. When you use Shopify Payments, you are using Stripe's infrastructure for processing transactions, but you manage everything through your Shopify admin instead of a separate Stripe dashboard.
Is it cheaper to use Stripe or Shopify Payments?
For most merchants, Shopify Payments is cheaper. While both services charge similar processing fees (like 2.9% + $0.30), Shopify adds an extra "third-party transaction fee" (0.5% to 2.0%) if you use a standalone Stripe account. You avoid this extra fee by using Shopify's integrated system.
Can I use Stripe and Shopify Payments at the same time?
Generally, no. You cannot use both as your primary credit card processor on the same Shopify store. You must choose one. However, you can use other third-party providers alongside your primary gateway for specific needs like PayPal, Apple Pay, or Buy Now Pay Later services. If you need to hide PayPal or the Express Checkout buttons at checkout, see Hide PayPal Express Checkout Button in checkout for details and limitations.
What happens if I am in a country where Shopify Payments isn't available?
If you are in an unsupported region, you will need to use a third-party gateway. Stripe is often the most popular choice in these areas. You will have to pay Stripe's processing fees plus Shopify's third-party transaction fee, but this is the standard way to accept payments in those markets.