Shopify Built-in Payment Gateway vs. Third-Party Payment Processors: The Comprehensive Comparison

When it comes to setting up an online store, one of the critical decisions you’ll face is choosing the right payment gateway. The payment gateway you select will directly impact your customers’ shopping experience and the efficiency of your eCommerce operations. In this comprehensive guide, we’ll delve into the comparison between Shopify’s Built-in Payment Gateway, known as Shopify Payments, and Third-Party Payment Processors. Let’s explore the features, functionalities, advantages, and disadvantages of each option, so you can make an informed choice that aligns with your business goals.

Brief History and Development of Shopify’s Built-in Payment Gateway

Before we dive into the comparison, let’s take a quick look at the origin of Shopify Payments. Launched in 2013, Shopify Payments was developed by Shopify itself to streamline the payment process for its users. It was created to integrate seamlessly with Shopify stores, providing a native and unified payment solution for merchants.

Features and Functionalities

Shopify Payments boasts an array of features tailored to enhance the user experience. It provides a simple and hassle-free checkout process, reducing cart abandonment rates and increasing conversions. With its seamless integration, customers can complete transactions without being redirected to external payment gateways.

Transaction Fees

One significant advantage of Shopify Payments is the potential cost savings on transaction fees. When merchants use Shopify Payments as their payment gateway, they may be eligible for discounted transaction rates compared to third-party processors. However, it’s essential to be aware that these fees can vary based on the Shopify plan you are on.

Payment Processing Time

In terms of payment processing time, Shopify Payments ensures swift transactions, typically depositing funds directly into the merchant’s account within a few business days. This quick payout can be advantageous for maintaining cash flow and optimizing your business operations.

Security Features

Security is a paramount concern in eCommerce, and Shopify Payments takes it seriously. The built-in gateway complies with Payment Card Industry Data Security Standard (PCI DSS) requirements, providing a secure environment for processing sensitive customer information. This instills trust and confidence in your customers, leading to more successful transactions.

Supported Currencies and Countries

Shopify Payments supports multiple currencies and is available in various countries worldwide. This global reach allows merchants to cater to a broader audience, facilitating international expansion and growth opportunities.

Pros and Cons

As with any payment solution, Shopify Payments comes with its own set of advantages and limitations.

Advantages of Using Shopify Payments

  • Seamless integration with Shopify stores for a cohesive checkout experience.
  • Potential cost savings on transaction fees, depending on the Shopify plan.
  • Swift payment processing, ensuring timely fund deposits.
  • Robust security features, meeting PCI DSS requirements.
  • Global reach, enabling merchants to tap into international markets.

Disadvantages or Limitations

  • Availability may be limited to specific countries, depending on the merchant’s location.
  • Some high-risk industries may not be eligible for Shopify Payments, leading to the need for alternative solutions.

Overview of Third-Party Payment Processors

1. What Are Third-Party Payment Processors?

Third-Party Payment Processors are external payment gateways not directly affiliated with the eCommerce platform, such as Shopify. These processors offer a range of payment options and services and can be integrated into the Shopify store using various third-party apps and plugins.

2. Popular Third-Party Payment Processors

Numerous third-party payment processors are available in the market today, each with its own set of features and benefits. Some well-known examples include PayPal, Stripe, Square, and Authorize.Net.

3. Features and Functionalities

Third-Party Payment Processors come with a wide array of features, catering to diverse merchant requirements. They often offer multiple payment methods, including credit cards, digital wallets, and more, giving customers flexibility and convenience during checkout.

4. Transaction Fees

The transaction fees associated with third-party payment processors can vary depending on the provider and the specific plan chosen by the merchant. It’s essential to carefully compare and consider these fees to ensure they align with your budget and expected transaction volume.

5. Payment Processing Time

The payment processing time for third-party payment processors can vary, with some offering faster payouts than others. It’s crucial to review the processing time and consider how it aligns with your business needs, especially in terms of cash flow management.

6. Security Features

Similar to Shopify Payments, reputable third-party payment processors prioritize security measures. They employ encryption and other security protocols to safeguard sensitive data, instilling trust among customers and merchants alike.


Third-Party Payment Processors come with their own set of benefits, making them a popular choice for many merchants.

  • Diverse payment options, accommodating a broader range of customer preferences.
  • Wide availability and compatibility with various eCommerce platforms.
  • Robust security measures to protect sensitive information.
  • Flexibility to choose between multiple payment processors based on pricing and features.


However, there are also some potential drawbacks to consider when using third-party payment processors.

  • Additional transaction fees that may impact profit margins.
  • The need for integration with Shopify through third-party apps, which can sometimes lead to technical complexities.
  • Potential redirects during the checkout process, which may affect the user experience.
Shopify Built-in Payment Gateway vs. Third-Party Payment Processors

Comparative Analysis: Shopify Payments vs. Third-Party Payment Processors

In this section, we’ll conduct a head-to-head comparison between Shopify Payments and Third-Party Payment Processors based on essential factors.

1. Transaction Fees Comparison

Shopify Payments often offers competitive transaction rates for merchants using their platform. However, third-party payment processors may have different fee structures, and it’s essential to evaluate them carefully. Depending on your sales volume and business model, third-party processors may offer attractive pricing plans tailored to your needs.

2. Security Features Comparison

Both Shopify Payments and reputable third-party payment processors prioritize security and encryption to protect customer data. Ensure that the processor you choose adheres to stringent security standards to maintain customer trust.

3. Ease of Integration with Shopify

Shopify Payments enjoys seamless integration with the platform since it is built-in and maintained by Shopify itself. On the other hand, third-party payment processors may require additional apps or plugins to achieve the same level of integration. It’s essential to select a processor with a user-friendly integration process that aligns with your technical capabilities.

4. User Experience Comparison

A smooth and hassle-free checkout process is vital for customer satisfaction and higher conversion rates. Shopify Payments provides an integrated experience, potentially reducing friction during checkout. However, some third-party processors may offer equally seamless experiences, depending on the chosen app or plugin.

5. Global Reach Comparison (Supported Currencies and Countries)

Shopify Payments has expanded its global reach, supporting multiple currencies and operating in numerous countries. Third-party payment processors, too, often offer extensive global coverage, allowing merchants to reach international audiences. Ensure the processor you select supports the countries and currencies relevant to your target market.

Factors to Consider in Choosing Between Shopify Payments and Third-Party Payment Processors

Now that we’ve explored the strengths and limitations of both options, let’s delve into the essential factors to consider when making your decision.

1. User Convenience

If you prioritize a seamless user experience and wish to avoid potential redirects during the checkout process, Shopify Payments may be the better choice. However, some third-party processors offer equally smooth integrations, making them viable alternatives.

2. Customer Support

Consider the level of customer support offered by each payment gateway. Timely assistance in case of technical issues or payment disputes can significantly impact your business operations.

3. Compliance with Regulations

Ensure that the payment gateway you choose complies with relevant regulations and security standards to protect your business and customers’ data.

Summary of Key Points

  • Shopify Payments, as a built-in gateway, offers seamless integration and potentially cost-effective transaction fees.
  • Third-party payment processors provide diverse payment options and compatibility with various eCommerce platforms.
  • Consider transaction fees, security features, ease of integration, user experience, and global reach when making your decision.

Personal Recommendation and Rationale

After thorough analysis, the ideal payment gateway for your Shopify store depends on your specific needs and priorities. Shopify Payments is an excellent choice for merchants seeking a seamless, integrated solution with potential cost savings. However, third-party payment processors can be advantageous for those who require diverse payment options or have specific global reach requirements.

Encouragement for the Reader to Choose the Right Option Based on Their Unique Needs and Circumstances

In conclusion, take your time to evaluate both Shopify Payments and third-party payment processors based on your business requirements. Consider factors like transaction fees, security, user experience, and global reach to make an informed decision. Remember that the right payment gateway can significantly impact your eCommerce success, so choose wisely.

If you’re ready to elevate your eCommerce business and stay ahead in the digital race, consider leveraging MarkLoops’ unmatched Headless Shopify Development Services. With our expertise, you can optimize your Shopify store, ensuring a seamless shopping experience for your customers. Act now and embrace the future of eCommerce with MarkLoops.


What is the key difference between Shopify’s built-in payment gateway and third-party payment processors?

The main difference lies in the ownership and integration of the payment gateway. Shopify Payments is a built-in solution created by Shopify, seamlessly integrated into their platform. Third-party payment processors, on the other hand, are external gateways integrated with Shopify through third-party apps or plugins.

Are there any transaction fees associated with using Shopify Payments vs. third-party payment processors?

Yes, there are transaction fees associated with both options. Shopify Payments may offer discounted transaction rates depending on the Shopify plan, while third-party processors have their own fee structures, which can vary based on the provider and plan.

Which offers a better checkout experience: Shopify Payments or third-party processors?

The checkout experience can be equally smooth with both options, depending on the specific third-party processor used and its integration with Shopify. Shopify Payments, being built-in, offers a more streamlined experience with potential advantages in reducing redirects during the checkout process.

Can I use both Shopify Payments and third-party payment processors in my online store?

Yes, it’s possible to offer multiple payment options on your Shopify store by integrating both Shopify Payments and third-party payment processors. Providing diverse payment methods can enhance the shopping experience for your customers.

Are there any limitations on the types of products I can sell using Shopify Payments vs. third-party payment processors?

Yes, there might be some limitations depending on your business model and the industry you operate in. Shopify Payments may have restrictions on certain high-risk industries, which may require you to consider third-party payment processors to accommodate specific product categories.

For more information about Shopify and its benefits, check out MarkLoops’ article on “Why Shopify is the Best eCommerce Platform.”

To ensure the security of your Shopify store, explore MarkLoops’ comprehensive guide on “Shopify Security: Its Importance, Checklist, and Tools.”

In conclusion, choosing the right payment gateway is a critical decision for your eCommerce success. By considering your unique needs, prioritizing user experience, and evaluating the advantages and limitations of both Shopify Payments and third-party processors, you can make an informed choice that sets your online store on the path to growth and prosperity.