Shopify Payments is a payment gateway that can compete with many providers within the target scope. Established in 2013, the company was "the first and only eCommerce platform to offer the fully integrated payment solution for the online stores."
Today, Shopify payment provider features plenty of lucrative advantages for the eCommerce business. Flexible subscription plans and competitive transaction fees, certified security standards, and 3D secure checkouts – no wonder the system is trusted by more than 2,500,000 merchants in over 175 countries across the globe.
A reliable transaction processing system is one of the key processes to consider once launching a Shopify eCommerce store. Though it seems pretty challenging at first, the properly selected payment processor can impact the business performance and its revenues, ensuring a fast and secure experience for both clients and business owners.
In this article, we’ll explain the basics of implementing the best payment methods for Shopify, including how to choose the right payment processing solution, what is the best payment gateway for Shopify, and effectively integrating it into your platform.
Additionally, GenovaWebArt experts will introduce the major alternatives to Shopify payments, as well as how to get the system set quickly, efficiently, and without compromising your business.

Table of Contents

10 Best Shopify Payment Methods

Having discussed the advantages of features of the best payment gateways for Shopify, it's time to look deeper at the options, which are currently available on the market. Below you'll find an overview of popular Shopify alternative payment methods to help you choose the best one based on pricing specifics and features offered.

1. Shopify Payments

One of the most cost-efficient, in-built solutions for Shopify websites, that can easily manage and process payments without involving any third-party solution. Its best features are real-time monitoring, advanced security, comparatively low processing fees, and flexible subscription plans. 
However, keep in mind that Shopify is available in a restricted number of countries and may withhold your money temporarily, which is not always convenient for business owners.

2. Shop Pay

Another common payment option for Shopify websites is transparent and easy to set, yet fits both local and international transactions. Similar to PayPal, it supports various payment options and currencies and has a highly customizable checkout flow. 
Additionally, you don't have to pay for the setup or cancellation with Shop Pay! But this platform has a comparatively steep learning curve and is only available in up to 40 countries, which might not fit your eCommerce model.

3. PayPal

A decent alternative to Shopify payments trusted by over 220 million customers across the globe. It features both paid and free plans for Shopify store owners, supports a wide range of currencies, and has an intuitive mobile interface. 
Paypal's most notable drawback is the inconsistent customer service and periodic account blocking for whatever reason.

4. Klarna

Unlike other solutions, Klarna is appreciated for a buy now, pay later structure, which is highly applicable among Commerce with expensive products. It offers a seamless checkout experience, easy integration, and low transaction fees. Also, Shopify store owners can get a complete payment at checkout!
But once you've got any issues or need a consultation, interacting with the support team might be really tricky and won't always fulfill your requests.

5. Amazon Pay

Amazon Pay is an excellent payment alternative for the Shopify store that features high-end security with the fraud protection system and is supported across a wide range of countries. Moreover, it offers a highly convenient customer experience during checkout, as it allows automatically inputting the customer details. 
But, this option requires having an Amazon account and has certain restrictions due to compliance with Amazon's regulations.


The main feature that makes stand out from the competitors is the robust fraud prevention and security attributes. Furthermore, the platform supports most of the common payment options like Visa, JCB, MasterCard, American Express, etc, and supports the digital payment options – ApplePay and GooglePay.
However, it features comparatively high service rates and a complicated user interface, which might seem confusing at first.

7. Opayo

Opayo is known among the merchants in the US and UK as a reliable payment system for Shopify. It has online and offline modes and is extremely reliable and secure when handling customer transactions. 
One of the major problems of this solution is a durable account verification that can take up to 5 weeks, during which any transaction cannot be processed.

8. Verifone

Though not as popular as others listed, Verifone is a flexible payment solution that can adjust to your current business needs. It has free signup, charges for each transaction processed, and offers a convenient tax calculation that can't be overlooked. 
However, its system structure doesn't fit Shopify store owners who sell products considered to be high risk.

9. WorldPay

WorldPay will best fit the merchants needing a solution for online, over-the-phone, and credit/debit card payment methods. The system is available in over 100 countries and features top-notch fraud protection and a straightforward set up. 
However, it offers only two subscription plans, and you might need to request a consultation to get more details about the system performance.

10. Square

Square is highly popular among Shopify store owners for its helpful extensions and different payment structures, including donations, membership fees, appointment scheduling fees, and standard transactions. The payments are usually received within 1 to 2 days, which is good from the business perspective. 

Nevertheless, its accounts may experience stability issues, and the platform is comparatively expensive for large-scale eCommerce businesses. 

As you can see, there are numerous Shopify payment processing options to choose from. You just need to select the one depending on your project’s needs and business objectives.

Why Do You Need a Shopify Payment Solution?

Payment Methods on Shopify & Its Integration - GenovaWebArt blog article, main image

A payment processing system is an integral component of any eCommerce platform. Its primary purpose is to capture the data, ensure the funds are available and get a merchant paid. A reliable and effective payment solution also influences the SEO optimization of your Shopify store.

Accepting Online Payments

Shopify payment processing solutions refer to the methods that allow websites with Shopify subscription to accept payments online. These options enable conducting secure, stable, and transparent online transactions with ease using only a credit card, which is convenient for clients and business owners.

Processing the Transactions

The payment provider starts processing the transaction once the product purchase is initiated. Shopify payment providers send the confidential details of the credit card owner to the bank issuer and get a response about the transaction outcome. They can also bring more security to large transactions, implementing more stringent measures to verify the customer's account before processing the transaction.

Appearing as a Reliable and Secure Store to Customers

Choosing the best payment provider for a Shopify website with the most efficient features on board can not solely add to the payment speed and security. From the standpoint of a business owner, it can also significantly affect the net revenues of your eCommerce site, depending on the service fees and selected subscription plans.

Key Benefits of Shopify Payment Methods

Key Benefits of Shopify Payment Methods, Illustration for Blog Article - Payment Methods on Shopify

Having a modern and functional payment system on your Shopify website has many lucrative advantages for both eCommerce owners and their clients. Getting to all the benefits of Shopify payment options will help you to evaluate the potential of this solution for your business. Below you'll find some of the most notable perks of implementing alternative payment methods to a Shopify website.

Complete Payment Flexibility

Accepting various payment options, such as credit cards, PIN debit, EMV chip, and contactless transactions such as credit/​debit tap, Apple Pay, and Samsung Pay, can make your business more agile and customer-focused. Additionally, it ensures a seamless shopping experience with minimum hassle around the payment processing for your clients.

Faster Transaction Speed

Shopify payment providers enable improved money flow. It allows getting paid within 24 hours after the transaction.

Secure Payment and POS Integration

There is no need to enter the price. Every transaction goes to a payment terminal using POS, making the service convenient and fast. Additionally, most Shopify payment options support non-integrated payment systems and automatically update the invoices once the payment is tendered.

Remote Terminal Management

Merchants can manage all aspects of their payment options using a single platform, anytime and from nearly anywhere. This allows for timely detection, eliminates payment issues, and blocks suspicious activity within the network to prevent fraud.

Access to Premium Services

Most of today's payment systems offer advanced premium solutions which are costly or unavailable to the average business. Most Shopify payment providers feature affordable solutions and flexible plans for any budget. It allows eCommerce platforms to implement advanced solutions into their workflow at reasonable costs.

All these advantages of payment providers for Shopify can add more to the convenience of payment processing, improve the transactions flow and make your business more competitive within the target niche.

Features to Consider When Choosing a Shopify Payment Method

Once you've decided to choose a Shopify payment provider, you'll probably be drawn to various parameters and characteristics of the payment gateway. Nevertheless, there are still some essential features to mind before making your final choice:

  1. Customer Shopping Experience – make sure the payment system should provide a comfortable payment process for each of your clients. Consider choosing some of the Shopify alternative payment methods.
  2. Geographical Location of Target Market – opt for the solution that works for your target market
  3. Transaction Fees – compare the pricing to define the most cost-efficient option at the decent quality
  4. Accepted Payment Cards – choose the system that is compatible with most of the available credit and debit card providers (such as MasterCard, VISA, and American Express)
  5. Worldwide Availabilityensure the Shopify payment system potentially works for the global audience and allows the configuration of Shopify market settings
  6. Availability of Fraud Detection Features – check whether the payment method is secure, risk-free, and can timely determine the payment fraud

    These aspects will help to define the best payment method for Shopify, which can ideally serve any eCommerce business.

How to Integrate Payment Methods on Shopify

How to Integrate Payment Methods on Shopify, Screenshot for Blog Article - Payment Methods on Shopify

In fact, integrating the payment methods in Shopify is pretty easy and doesn't require any specific expertise. Whether you decide to do it yourself or entrust it to professionals, implementing the payment system can be performed in just three essential steps:

  • Select the best payment method for Shopify based on the core business preferences and customer needs
  • Connect payment method to your Shopify store (go through "Settings" > "Payment Providers" > "Add a Provider", then activate Shopify Payments or choose any of the best third-party payment providers for Shopify)
  • Make settings for the selected payment method by filling out the online form that you need to fill out with relevant information

After these steps, your clients can start making payments on your site!

Shopify Payments vs. Third-Party Providers

The final question to answer when analyzing the best Shopify payment methods is which option is the most effective from the eCommerce business perspective. The final decision will mainly depend on your target audience, business goals, and the methods available. 

In our experience, the owners that are currently running a store on Shopify usually choose Shopify Payments. It's an excellent payment gateway for small to mid-sized businesses and can also be a decent option for large-scale platforms in some cases. Shopify Payments are simple in use, come with fewer charges and provide a standalone payment solution at high-grade security. 

Growing businesses that are focused within a certain niche, or have already obtained a huge customer base can also consider alternatives to Shopify payments. 

In this case, the key elements to consider will be the customer preferences, pricing, and complexity of setting up and maintenance. Knowing all these parameters, business owners can make a profitable, data-driven decision for their eCommerce platform. 

While choosing a Shopify payment method, make sure it supports the Express Checkout. This option allows customers to quickly get a product without inserting lots of personal information, significantly reducing the abandoned cart rate. The Shop Pay solution has a good Express Checkout feature with many customization options.

Need to Personalize Your Shopify Store? Contact GenovaWebArt!

Setting up the best payment processor for Shopify takes some time, but is surely worth the effort. By choosing the right third-party application for your Shopify website, you can ensure excellent customer support and experience with the maximum profit for your business. 

We do hope that this guide has given you a basic idea of Shopify payment systems, as well as how to effectively implement them into your business. At the same time, you can now evaluate the potential of different solutions and better understand which one can work for you. 

If you still have any questions concerning the Shopify payment methods or want to discuss which of the providers will be the most efficient for your business, contact GenovaWebArt! Our experts know all the secrets of setting up an efficient payment processing system and can help you make the most of your Shopify business right away! 

We have already helped numerous projects select and integrate the right Shopify payment providers.

Thus, make sure to check our portfolio to see how we helped NYC-based sportswear brand Ten Thousand and beauty brand Winky Lux develop their eCommerce websites.

Frequently Asked Questions

How to improve the customer experience in the Shopify store using the payment method?

There are multiple ways to improve the conversion funnel with payment processing. First, implement different payment options of the client’s choice and reduce the number of steps in the checkout process. Additionally, allow payments without requiring an account and ask for the essential information only.  Regardless of the payment method used, make sure to provide guarantees on the payment security and privacy to gain your client's trust.

How do payment methods in the Shopify store affect sales growth?

Using convenient payment options on a Shopify website can significantly reduce the wait time, minimize the cart abandonment rate and increase customer satisfaction. In turn, business owners can gain better revenues and more cost-efficient platform maintenance. The last advantage is mainly caused by implementing the Shopify payment platform with the most profitable charging fees and flexible subscription plans.

Do I need Stripe if I have Shopify?

Shopify has a native payment processing solution – Shopify Payments – which is powered by its alternative, Stripe. When launching a Shopify store, business owners are free to use any preferable option.  However, if using the third-party payment gateway, Shopify will charge extra fees for connecting to the processor, such as, for instance, PayPal or Stripe.

Are Shopify Payments better than PayPal or Stripe?

Shopify Payments can be an excellent option for business owners who already use Shopify as an eCommerce platform, as it allows avoiding the extra fees of 1% to 2% per transaction.  Additionally, unlike the over options, Shopify has a wide range of different subscription plans, which adds to the flexibility and scalability of your eCommerce business. Finally, this payment system allows tracking transaction processing in real-time, which is not supported by PayPal and Stripe.

Is it worth implementing the Shopify payment method?

Except for the chargeback fee, Shopify itself doesn’t charge any add-on monthly fees, payment security fees, hidden fees, or setup fees on its payments service. This makes it an attractive option among the payment processing solutions offered on the market.

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