Tom-Chris Emewulu
Chargeflow's Digital Evangelist
Table of contents

Are you looking for the best payment processor for Shopify? You’re not alone.

Choosing the right payment processor for your eCommerce store is fundamental to business success. It directly impacts customer experience, conversion rates, overhead costs, and operational efficiency.

For Shopify merchants, the choice of payment processing partner holds even greater weight. Shopify has specific conditions merchants must meet, including minimizing fraudulent transactions. A good payment processor is pivotal to achieving that objective.

If businesses exist to make money, working with the wrong payment processor is like making bricks without clay.

Keep reading as we highlight the best payment processors for Shopify. We’ll uncover the features, benefits, and how they can contribute to your business’s growth and success.

What is a Payment Processor for Shopify?

A Shopify payment processor is an intermediary service between a merchant (i.e., a Shopify store owner), the customer, and the customer’s payment method (such as credit card, debit card, crypto, etc.) to facilitate online transactions.

Such intermediary responsibility includes, but is not limited to, the following:

  • Managing transaction details securely: When a customer buys from your Shopify store, the payment processor collects the transaction details from the payment gateway in an encrypted channel.
  • Authentication and payment authorization handling: After verifying payment information and ascertaining sufficient credit, the payment processor transmits payment details to the card issuer for transaction approval.
  • Transaction processing: Once the issuing bank authorizes the transaction, the payment processor initiates funds transfer from the customer's bank account or credit card to the merchant's account. The purchase amount is deducted from the customer's account and credited to the merchant.
  • Payment settlement: After transaction processing, the payment processor settles the funds into the merchant's bank account. Payment settlement usually occurs within a few business days, depending on the processor and the merchant's bank.

The extent to which your payment solution meets your customers’ expectations depends on the payment processor you work with. It pays to do proper due diligence before choosing a payment option for your business.

What to Look for in a Payment Processor for Shopify

There are several Shopify payment processors in the market nowadays. Each payment solution has distinct features that suit different business types.

Understanding these unique benefits – and the trade-offs you must make – is vital for all merchants. This section highlights some of the non-negotiable features to look for in an ideal payment processor for Shopify.

Seamless Integration

Ideally, you want a Shopify payment process with a plug-and-play onboarding strategy. eCommerce is about speed and effectiveness. Everything moves fast.

You want to ensure compatible integration without overhauling your system to accommodate the payment service. That includes keeping ongoing maintenance costs to the barest minimum while ensuring excellent customer experience for your shoppers.

Payment Security

Fraud risk is among the reasons for cart abandonment. Research shows that about 18% of shoppers abandon their carts due to personal or payment information security concerns. Payment processors attempting to tackle security with lengthy or complicated checkout processes have also contributed to increased cart abandonment for eCommerce.

Up to 28% of shoppers have abandoned carts due to complicated checkout processes. So you want a payment processor for Shopify that assures payment security without sacrificing quick checkout.

Global Availability

An ideal payment processor for Shopify must offer global availability and multi-currency support. eCommerce is about reaching customers wherever they are. And one of the many benefits of selling on Shopify is the platform's expansive, global reach.

You limit your growth prospects if your payment provider lacks international currency support.

Availability of multiple payment methods

To cater to diverse customer preferences and increase conversion rates, you must allow buyers to pay how they want.

Providing flexible checkout options beyond credit/debit cards ensures convenience and trust. You accommodate different customer demographics and regional preferences. It also reduces cart abandonment rates, enhances customer satisfaction, and expands market reach.

Transparent fee structure

Do your research on fee structures before choosing a Shopify payment provider. Ensure you understand the company's payment policy. Some payment providers charge chargeback, statement, and cancellation fees in addition to the standard payment processing fees. Understand all costs upfront to make an informed decision.

Note: There are three main tiers for payment processing fees. These include set-up fees, maintenance fees, and transaction fees. Initial set-up fees vary across networks. Some payment providers offer waivers. Others charge up to $250 set-up fees. Maintenance fees typically range from $10 to $50. Payment settlement fees are generally 1% to 5% per transaction, accompanied by a flat fee of 25¢.

Timely settlement and account reconciliation

Rapid reconciliation and payout facilitates early fraud detection and regulatory compliance, enhancing transparency and operational efficiency. Sales is one thing. Accessing your funds is another.

Timely payment settlement means steady cash flow to finance overhead expenses. Ensure you have flexible payout scheduling before choosing your Shopify payment processor. Some payment providers release your funds the next business day. This is especially vital for SME businesses.

Best Payment Processors for Shopify

Payment processing is a big part of every business. But choosing the best payment processor for Shopify doesn’t have to be a nightmare. Below are helpful analyses to help make it simple, a stress-free aspect of eCommerce business.

Shopify Payments

Shopify Payments is a native payment system from the eCommerce behemoth. It's a seamless payment solution enabling instant acceptance of credit cards and other popular methods upon signup.

It's integrated directly into Shopify stores and included in your subscription plan for a smooth checkout experience. That eliminates the need for complex third-party integrations. The Shop Pay functionality allows shoppers to swiftly checkout using phone numbers, keeping payments and sales data unified within the Shopify ecosystem.

Furthermore, Shopify Payments offers a clean interface, competitive rates, and multiple payment options. Shopify also refunds the $15 chargeback fee if you win a dispute.

Shopify Payments fees are between 2.4% to 2.9% of the purchase amount, with a flat 30¢ per transaction. These fees typically include interchange fees, simplifying cost calculation without separating them as an additional charge.

Upsides of using Shopify Payments as your payment processor

  • It requires no third-party integrations.
  • There are no incremental or hidden costs.
  • The UI is clean, and the platform is intuitive to use.
  • It comes with Shopify’s security system; you know what in the world is going on with your transactions.
  • You can collect payments however customers want and in different currencies.
  • The service is included in your subscription package, meaning you pay no extra setup fees.
  • With one-click integration, you can quickly start accepting payments without hassle.

Downsides of using Shopify Payments as your payment processor

  • Shopify Payments is not currently available in all countries.
  • You pay a fee to use third-party payment gateways.
  • You pay a premium to use advanced features like custom reports and analytics.
  • The strict chargeback and fraud policy means certain businesses can’t use the service.


Stripe is a popular payment processor for Shopify. The payment giant is on a mission to power payments for the eCommerce economy. They seek to help eCommerce businesses reduce friction for customers. They achieve this by optimizing your checkout flow and helping you accept payments globally.

Stripe is renowned for its robust API and wide-ranging features, making it suitable for businesses of all sizes. They provide versatile, customizable, and secure solutions for online and in-person transactions worldwide. With robust integration options, scalability for businesses of all sizes, and advanced analytics, Stripe enhances checkout experiences and supports extensive global reach while offering reliable customer support and developer-friendly tools.

With Stripe's Instant Payouts, you can access funds within 30 minutes after transactions at a 1% and 50 cents per order fee. Stripe charges no monthly fee. Transaction fees are around 2.9% plus 30 cents per transaction, with a 1% fee for international and currency conversion transactions.

Upsides of using Stripe as your payment processor for Shopify

  • Stripe API and developer-friendly tools allow for seamless integration.
  • The instant Payout option makes transaction funds available when needed.
  • The payment system makes sense for eCommerce business: flat-rate pricing and zero fees for setup or cancellation.
  • It’s extensively customizable for tailored user experience and payment workflows.
  • Multiple payment options and access to 135 currencies mean your buyers have more choice.
  • It has advanced security features and compliance with industry standards to protect payment information.
  • Stripe payment scales with businesses of all sizes, from startups to large enterprises, accommodating growing transaction volumes.

Downsides of using Stripe as your payment processor for Shopify

  • Stripe is not currently accessible in all countries.
  • The platform has stringent chargeback and fraud policies.
  • It charges additional fees for features like Instant Payouts and currency conversions.
  • It requires some technical knowledge for integration and customization, which can be challenging for non-technical users.


There’s a reason PayPal currently has 426 million active users​​. The platform is a globally recognized digital payment solution that revolutionized online transactions. Merchants love PayPal as a payment processor for Shopify because PayPal allows you to add Venmo to Shopify. Venmo has over 90 million active users, and it’s popular among the younger, mobile, and social demographic.

PayPal also offers pay-later options and even cryptocurrencies. PayPal's buy now, pay later solutions have driven over 2X more purchases than PayPal's standard checkout.

Security features such as buyer and seller protection enhance trust. They mitigate fraud risks for users. With its user-friendly interface, widespread acceptance, and robust buyer and seller protections, PayPal remains a preferred choice for millions globally.

That said, PayPal imposes a non-refundable $20 chargeback fee. They do not refund transaction fees on customer returns, which is important to note for businesses dealing with frequent eCommerce returns. PayPal has also created Braintree to cater to recurring payments.

Upsides of using PayPal as your payment processor for Shopify

  • PayPal supports payments in over 200 countries and accepts multiple currencies, including Venmo and crypto, facilitating international sales.
  • Many customers prefer PayPal due to its buyer protection policies, which help you build trust and reduce cart abandonment.
  • The setup is seamless, allowing for effortless payment management.
  • With PayPal's mobile-friendly checkout options, customers can purchase easily on any device – giving you 25% better conversion rates.

Downsides of using PayPal as your payment processor for Shopify

  • PayPal charges higher transaction fees, compared to Stripe, especially for international transactions and currency conversions.
  • PayPal is renowned for placing holds on funds or freezing accounts temporarily, which often disrupts cash flow for businesses.
  • Users have reported challenges accessing timely customer support, especially for account-related issues or disputes.
  • PayPal charges a non-refundable chargeback fee, which becomes a burden with rising dispute rates.


Klarna helps merchants offer affordable transactions by breaking down costs into short-term, interest-free installment loans. Customers also have access to traditional financing options.

Merchants regard Klarna as one of the top complementary Shopify payment solutions for integrating into your store. Merchants pay Klarna to allow customers to buy now and pay later to encourage increased sales.

Klarna offers a one-time-use virtual card for online retailers that accept prepaid Visa cards. This card allows buyers to conduct online transactions wherever prepaid Visa cards are accepted.

Shopify automatically enables the Klarna payment option when you set up Shopify Payments, provided Klarna has approved your business. Customers can then choose Klarna as a checkout option.

If you issue a refund through Klarna, Shopify refunds the processing fee they originally charged. Transaction fees for payments from regions such as the United Kingdom or Ireland are 2.49% + 0.20 GBP per transaction.

Upsides of using Klarna as your payment processor for Shopify

  • Klarna's "buy now, pay later" model has been recorded to significantly boost conversion rates by offering customers flexible payment options.
  • The seamless and user-friendly checkout experience improves overall customer satisfaction.
  • Klarna bears the credit and fraud risk associated with transactions, which gives peace of mind to merchants.
  • They provide merchants with detailed analytics and insights into customer purchasing behaviors and payment preferences.
  • Klarna often runs promotional campaigns and marketing initiatives to promote businesses using its payment options.

Downsides of using Klarna as your payment processor for Shopify

  • Klarna's transaction fees are higher, compared to traditional payment processors like PayPal, especially for smaller merchants or those with lower sales volumes.
  • Approval by Klarna is required before integrating their payment options, meaning potential delays or rejection based on their assessment criteria.
  • Offering "buy now, pay later" options increases payment default risks, leaving the merchant potentially liable for unpaid balances.
  • Klarna isn’t as widely recognized or trusted in all regions compared to more established competitors.
  • Reported customer service fluctuations can affect business operations.


Square's payment solution helps merchants accept online and offline payments. It's a suitable choice for vendors operating both an eCommerce store and a physical storefront.

Square offers various integrative extensions for Shopify, complemented by a dashboard that enables transaction monitoring, cash flow projection, and real-time inventory tracking.

Shopify store owners benefit from Square's versatile payment structures. It accommodates donations, membership fees, appointment scheduling fees, and standard transactions. Developers can use prebuilt Square Checkout APIs or create custom solutions using Square Web Payment SDKs. Square Cash App further enhances the workflow with excellent integration capabilities.

Transactions on Square are highly secure, as the platform is PCI compliant and uses end-to-end encryption. Also, payments are swiftly deposited into your bank account within one to two days.

Square pricing is generally favorable. Square applies a standard transaction fee of 2.9% + $0.30 per transaction. Advanced features, including analytics and marketing tools, come in a premium plan starting from a $12 monthly fee.

Upsides of using Square as your payment processor for Shopify

  • Square enables seamless integration between your online Shopify store and physical retail locations, allowing you to manage all sales channels from one platform.
  • Square offers several tools beyond payment processing, including inventory management, customer relationship management (CRM), and analytics, simplifying operations for Shopify merchants.
  • Besides credit cards, customers can pay with mobile and Square's payment solutions like Square Installments.
  • Square is PCI-compliant and uses advanced encryption to protect transactions and customer data.
  • There are no monthly fees for using Square with Shopify, making it cost-effective for businesses of all sizes.
  • Square integrates with over 100 shopping carts and can process transactions in 87 different currencies across 15 languages.

Downsides of using Square as your payment processor for Shopify

  • While Square integrates with Shopify, it may not offer the same level of seamless integration compared to Shopify's native payment processors.
  • Square has been known to impose holds or reserves on a merchant's funds if it detects unusual activity or transactions.
  • Square is primarily available in the United States, Canada, Australia, Japan, and the UK.
  • Square has mixed customer reviews, probably due to stringent fraud policies, especially for merchants in high-risk verticals.

Payline Data

Payline Data is helping merchants rethink how they process payments. The merchant service provider says they’re on a mission to solve the problems businesses face when collecting payments: inflexibility, inaccessibility, dishonesty, and complexity. Their strategy? Make payment collection online, in-store, and on mobile devices hassle-free, and give merchants tons of data to power their business.

They provide superior technology and resources to supercharge your business growth because they believe when you succeed, they succeed. From startups to Fortune 500s, Payline has extensive payment solutions tailored to its customer needs.

They provide cash advance opportunities to SMEs to lift working capital burdens and a seamless QuickBooks integration for better accounting. The Chicago-based fintech has been praised for its fantastic customer service.

Payline Data operates on flexible monthly contracts. Their pricing is competitive at interchange plus 0.4% + 10¢ per card-present transaction and 0.75% + 20¢ per card-not-present transaction.  

Upsides of using Payline Data as your payment processor for Shopify

  • Transparent pricing with a freemium option for the first month and month-on-month contracts for flexible payments.
  • Extensive solutions tailored to your business needs online, in-store, or mobile.
  • Secure terminals with a highly-rated payment suite that integrates seamlessly with established shopping platforms.
  • Value-added services like cash advances, QuickBooks integration, extensive insights, and excellent customer service.
  • Highly scalable, suitable for startups and established businesses.

Downsides of using Payline Data as your payment processor for Shopify

  • Initial setup might require some technical expertise.
  • Although very competitive, the pricing model may prove more confusing to some individuals than a flat-rate pricing model.
  • Payline Data primarily focuses on merchants operating in the United States.
  • Hardware integration might require extra budget and setup.

Maverick Payments

Maverick Payments offers a comprehensive payment processing service to promote business growth. Their white-labeled payments stack enables merchant partners to process credit cards, debit cards, ACH payments, and electronic checks.

Maverick says their services are available to businesses of all sizes. Their advanced payment platform simplifies payment collection with features like virtual terminals, hosted payment forms, and customizable developer APIs. They support international business and multi-currency transactions.

Maverick has a sophisticated fraud system designed to protect businesses, saving merchants time and money. This makes them suitable for companies that other processors consider high-risk. Maverick simplifies business operations with intuitive analytics that offer deep insights into payment processing metrics and customer behavior. Their dashboard goes beyond payment data, offering valuable information on industry trends, competitor analysis, and customer demographics to support informed business decisions.

Upsides of using Maverick Payments as your payment processor for Shopify

  • Maverick Payments integrates seamlessly with Shopify, ensuring a smooth setup process without disrupting operations.
  • They offer integrated POS systems with inventory management, sales reporting, and CRM.
  • Supports mobile payments via smartphones or tablets and is ideal for field operations or temporary retail setups.
  • Provides customizable gift card and loyalty program solutions for customer attraction and retention.
  • Maverick provides diverse financing options, including business loans, cash advances, and hybrid solutions.
  • Reputable for its security and scalability.

Downsides of using Maverick Payments as your payment processor for Shopify

  • Maverick's pricing isn't public as it varies by business and may include transaction fees, PIN debit fees, AVS fees, statement fees, and internet gateway fees.
  • Risk policy involves a $195 early termination fee, a $25 monthly minimum fee, a $25 chargeback fee, a $10 monthly service fee, and cash reserve or accounts freezing for suspicious transactions.
  • Maverick Payments isn't accessible in all countries.


Worldpay is a leading global provider of payment processing technology solutions. The company originally focused on card payments but has since evolved into comprehensive services, including online, mobile, and integrated payment solutions.

In 2017, Vantiv Inc. acquired Worldpay, expanding the company's presence, particularly in the United States. Worldpay operates in over 146 countries, serving a diverse range of businesses with secure and efficient payment processing. The company's website says they accept over 300 payment types in person.

Worldpay is recognized for its robust safety measures, ensuring that all its payment solutions meet stringent data security and encryption standards. Furthermore, Worldpay uses advanced fraud protection tools to safeguard personal information and restrict access to authorized individuals.

Upsides of using Worldpay as your payment processor for Shopify

  • Worldpay is PCI-compliant and uses sophisticated fraud prevention tools like two-factor authentication and data tokenization to protect against unauthorized transactions.
  • Seamlessly integrates with Shopify, providing a user-friendly interface and easy setup process.
  • Provides robust and reliable payment processing services, minimizing downtime and ensuring smooth transactions.
  • Supports multiple currencies and payment methods, allowing you to reach customers globally and accept payments in various forms.
  • Provides dedicated customer support, ensuring a positive experience for merchants and customers.

Downsides of using Worldpay as your payment processor for Shopify

  • Worldpay does not provide public information on expected costs and pricing.
  • Fraud policy might not favor all merchants due to monetary safety threats.
  • They charge early account closing fees ranging from $400 to $500.

Final Thoughts on Best Payment Processors for Shopify

Choosing the best payment processor for your Shopify store is a big decision. Your Shopify payment method decides how customers pay for transactions. It also determines how you protect customer information from fraud and data breaches.

Data breaches, leading to fraudulent transactions, are becoming commonplace these days. We see a recent case study with Arkansas-based Evolve Bank. Hence, when you choose a Shopify payment provider, you choose whom to trust with your transactions and business security.

I hope this analysis of the best payment providers for Shopify will help you make the right choice for your business. See how Chargeflow can help you stop eCommerce chargebacks before they happen or recover disputes on autopilot.


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