Can I Use My Own Merchant Account with Shopify? Understanding Your Options

Table of Contents

  1. Introduction
  2. Why Consider Your Own Merchant Account?
  3. Shopify's Native Payment Solution
  4. Using Your Own Merchant Account with Shopify
  5. Weighing the Pros and Cons
  6. Conclusion
  7. FAQ


Imagine you've just set up your online store on Shopify, filled with enthusiasm about the prospects of reaching customers worldwide and growing your business. However, as soon as you start considering the nitty-gritty of payment processing, a critical question arises: "Can I use my own merchant account with Shopify?" This question is crucial, whether you're a seasoned business owner switching to Shopify or a new entrepreneur venturing into the eCommerce world.

In this blog post, we will dive deep into the world of Shopify and its payment processing options, particularly focusing on using your own merchant account. By the end, you'll have a clearer understanding of not only how you can leverage your merchant account with Shopify but also the implications it brings, thereby allowing you to make an informed decision tailored to your business needs.

Why Consider Your Own Merchant Account?

Before delving into the technicalities, it's essential to understand what a merchant account is and why many businesses consider using their own. Essentially, a merchant account acts as an intermediary, enabling businesses to accept and process electronic payment card transactions. The allure of using one's own merchant account often lies in the potential for reduced processing fees, better control over transactions, and sometimes, more favorable terms based on a longstanding banking relationship.

Shopify's Native Payment Solution

Shopify offers its own integrated payment solution, Shopify Payments, which is designed to work seamlessly within the Shopify ecosystem. It supports various payment methods and currencies, ensuring a smooth checkout process for customers globally. With Shopify Payments, the need for a separate merchant account is technically bypassed, simplifying the payment process for many store owners.

However, not every business owner might find Shopify Payments aligning with their unique needs or financial considerations, leading to the exploration of alternative payment processing options.

Using Your Own Merchant Account with Shopify

Yes, you can use your own merchant account with Shopify. The platform is designed to be versatile, catering to a wide range of business requirements and preferences. Shopify supports the integration of over 100 different credit card payment providers, including direct providers (which allow customers to complete purchases directly on your online store without redirecting) and external providers (where customers complete purchases on a checkout page hosted outside of your online store).

Steps to Integrate Your Merchant Account:

  1. Evaluate Supported Payment Providers: First, identify if your merchant account provider is among the supported payment gateways on Shopify. This information is readily available on Shopify's official website or through their support team.

  2. Activate Your Provider: Once you've confirmed compatibility, you can activate or change your payment provider from the 'Payments' page in your Shopify admin. This process may involve entering specific account details or API keys provided by your merchant account's payment gateway.

  3. Consider the Implications: It's critical to recognize that using an external payment provider may incur additional fees. Shopify charges an extra commission on sales made through third-party payment gateways, on top of any fees your merchant account provider may levy. Assess these costs thoroughly to ensure it's a financially viable option for your operation.

  4. Opt for a Custom Solution if Necessary: In some cases, your business might require a more tailor-made solution. Shopify’s API allows for the development of custom integrations. This route, albeit potentially more complex and costly upfront, can provide unparalleled flexibility and control over your payment processing needs.

Weighing the Pros and Cons

Deciding whether to use your own merchant account with Shopify involves a careful consideration of various factors. Here’s a simplified breakdown:


  • Potential Cost Savings: Depending on your volume of transactions and the terms with your provider, you might save on processing fees.
  • Familiarity and Control: Working with a provider you're already comfortable with can offer greater oversight and customization of the payment process.


  • Additional Fees: Using an external gateway on Shopify incurs extra charges, which could add up, especially for businesses with high sales volume.
  • Complex Setup: Integrating and managing an external merchant account can introduce additional complexity in setting up and maintaining your store.


The flexibility to use your own merchant account with Shopify offers businesses a valuable option for tailoring their payment processing setup. However, this choice comes with its considerations, including potential extra costs and the need for a more hands-on approach to payment gateway management. By carefully evaluating your business's specific needs, transaction volume, and financial goals, you can make a well-informed decision on whether leveraging your own merchant account is the best route for your Shopify store.


Can any merchant account be used with Shopify?

Not all merchant accounts can be directly used with Shopify. It depends on whether the payment gateway associated with your merchant account is supported by Shopify.

What are the fees associated with using an external payment provider on Shopify?

Shopify applies an additional fee for transactions processed through external payment gateways, which varies depending on your Shopify plan.

Can I switch from Shopify Payments to my own merchant account anytime?

Yes, you can switch your payment provider from Shopify Payments to an external provider (and vice versa) directly from your Shopify admin settings, subject to any contractual terms with your current provider.