Shopify is one of the ecommerce world’s leading platforms, and for good reason. It’s feature-rich, (somewhat) easy to use, and affordable-ish.

But there are Shopify alternatives that give a little more freedom and a lot more bang for your buck.

Payment processing capabilities often determine which platform delivers the best value for your business. Let’s see the top Shopify alternatives and how their payment solutions impact your bottom line.

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Why Consider Shopify Alternatives?

Shopify charges additional transaction fees when you use third-party payment gateways – 2% for Basic plans, 1% for standard Shopify plans, and 0.5% for Advanced plans.

This fee structure pushes merchants toward Shopify Payments. This push limits your flexibility in choosing payment processors that might offer better rates or features for your specific business model.

Many alternatives eliminate these restrictive fee structures while providing comparable or superior functionality. BigCommerce, for instance, doesn’t charge any transaction fees regardless of which payment gateway you choose. This freedom allows you to shop around for the best processing rates and features without platform penalties.

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Top Shopify Alternatives and Their Payment Solutions

Alright, let’s get into what you came here for. Below is a short breakdown of each Shopify alternative.

BigCommerce

BigCommerce positions itself as an enterprise-ready platform that eliminates the transaction fee trap that catches many Shopify users. The platform supports around 65 payment gateways serving over 100 countries and more than 250 local payment methods.

Payment Processing Advantages:

• Zero transaction fees regardless of your chosen gateway
• Supports Buy Now, Pay Later options like Affirm and PayPal Pay Later
• Integrates with major digital wallets including Apple Pay, Amazon Pay, and Venmo
• Offers offline payment methods like bank deposits and cash on delivery

Pricing: Plans start at $39 per month, making it competitive with Shopify’s pricing while offering more payment flexibility.

Best For: Growing businesses that want freedom to choose and customize their payment processor and gateway without penalty.

WooCommerce

WooCommerce transforms any WordPress site into a fully functional e-commerce store. As an open-source platform, it provides unlimited customization options for payment processing. You can integrate virtually any payment gateway without platform restrictions.

It does offer its own payment processing and gateway, though it’s essentially a white-label of Stripe.

Payment Processing Features:

• Complete freedom to choose any payment processor
• No platform transaction fees – you only pay your chosen gateway’s rates
• Extensive plugin ecosystem for specialized payment solutions
• Support for subscription billing, installment payments, and complex pricing models

Pricing: The platform itself costs nothing, but you’ll pay for hosting, themes, and premium plugins. Total costs typically range from $500-$3,000 annually depending on your needs.

Best For: Businesses that want complete control over their payment processing setup and don’t mind managing technical aspects.

Squarespace

Squarespace excels at creating visually stunning online stores with its designer-quality templates. The platform’s payment processing approach differs significantly from Shopify’s model.

Payment Processing Structure:

• Squarespace Payments charges a standard 2.9% + $0.30 per transaction
• Transaction fees vary by plan: Commerce plans have 0% additional fees, while Business plans add 3%
• Integrates with major payment methods including credit cards, PayPal, and Apple Pay

The key advantage lies in Squarespace’s transparent fee structure. Unlike Shopify, you won’t face penalty fees for choosing alternative payment processors.

Pricing: E-commerce plans range from $25-$72 per month, generally more affordable than comparable Shopify tiers.

Best For: Creative businesses and brands that prioritize visual appeal and want a straightforward payment ecosystem.

Wix

Wix democratizes e-commerce with its intuitive drag-and-drop builder and competitive payment processing rates. Wix Payments offers a comparable solution to Shopify for small businesses.

Payment Processing Benefits:

• Wix Payments charges 2.9% + $0.30 per transaction with no setup or monthly fees
• No additional transaction fees for using the native payment system
• Supports multiple payment methods including credit cards, PayPal, and digital wallets
• Chargeback fees around $20, which is reasonable compared to industry standards

Pricing: E-commerce plans start at $29 per month, making it accessible for startups and small businesses.

Best For: Small businesses and entrepreneurs who want an affordable, user-friendly platform with transparent payment pricing.

Square Online

Square Online bridges the gap between online and offline sales, making it ideal for businesses with physical locations. The platform leverages Square’s established payment processing infrastructure.

Payment Processing Integration:

• Seamless integration with Square’s payment ecosystem
• 2.6% + 10¢ for in-person transactions, 2.9% + 30¢ for online sales
• No monthly fees for basic payment processing
• Real-time synchronization between online and in-store inventory

Pricing: Offers a free plan with transaction fees only, or paid plans starting at $29 per month when billed annually.

Best For: Businesses that operate both online and offline and want unified payment processing across all channels.

Custom-Built E-commerce Websites

Building a fully custom e-commerce website gives you complete control over every aspect of your store and payment infrastructure. Unlike platform-based solutions, custom websites eliminate all middleman fees and restrictions, allowing you to work directly with payment processors and negotiate the best possible rates.

Payment Processing Advantages:

• Direct API integration with any payment processor without platform restrictions
• Zero platform transaction fees – you only pay your chosen processor’s rates
• Complete customization of checkout flows and payment experiences
• Ability to implement multiple payment gateways simultaneously for redundancy
• Advanced features like split payments, complex billing scenarios, and custom fraud prevention

Integration Options:

Custom websites support multiple integration methods depending on your technical requirements.

Hosted payment pages redirect customers to secure processor-hosted forms, requiring minimal PCI compliance on your end.

Direct API integration keeps customers on your site throughout the payment process but requires full PCI DSS compliance.

JavaScript-embedded solutions provide seamless checkout experiences with dynamic payment fields that don’t require page reloads.

Technical Requirements:

Custom payment integration requires obtaining API credentials from your chosen processor and implementing secure server-to-server communication. You’ll need to establish a merchant account, ensure PCI DSS compliance, and thoroughly test all payment flows in sandbox environments before going live.

Pricing: Development costs typically range from $10,000-$100,000+ depending on complexity, but ongoing costs include only hosting, maintenance, and payment processing fees without platform penalties.

Best For: Established businesses with technical resources that process high volumes and want maximum control over their payment infrastructure and customer experience.

Stripe-Powered Alternatives

Several platforms leverage Stripe’s robust payment infrastructure while offering more flexibility than Shopify Payments. Stripe charges a standard 2.9% + 30¢ for online transactions and supports over 135 currencies.

Stripe Features:

• Accepts payments from customers worldwide while serving businesses in 47+ countries
• Transparent pricing with no hidden fees
• Advanced customization options for developers
• Comprehensive business performance insights and real-time statistics4
• Strong fraud protection and PCI DSS compliance

Platforms like custom-built solutions often integrate directly with Stripe, giving you enterprise-level payment processing without platform restrictions.

Payment Processing Comparison Table

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Making the Right Choice for Your Business

Choose BigCommerce if you process high volumes and want to avoid transaction fees while maintaining enterprise features. The platform’s payment flexibility becomes more valuable as your business scales.

Select WooCommerce if you need complete control over payment processing and have technical resources to manage the platform. The ability to negotiate custom rates with processors can significantly reduce costs for high-volume businesses.

Pick Squarespace if you prioritize design and want predictable payment costs without complex fee structures. The platform works well for creative businesses and brands selling premium products.

Go with Wix if you’re starting small and want the simplest path to online selling with competitive payment rates. The platform grows with your business without penalizing payment processor choices.

Consider Square Online if you operate physical locations alongside your online store. The unified payment processing across channels eliminates reconciliation headaches.

Develop your own site if you want granular control over every aspect of your site, payment ecosystem, and business.

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Beyond Basic Payment Processing

Modern e-commerce demands more than simple credit card processing. Consider these advanced payment features when evaluating alternatives:

Subscription Billing: Most digital businesses use subscription billing. Choose a solution that excels at recurring payments and complex billing scenarios.

International Sales: Platforms supporting multiple currencies and local payment methods expand your market reach significantly.

Buy Now, Pay Later: Integration with services like Affirm, Klarna, and PayPal Pay Later can increase conversion rates, especially for higher-priced items.

Mobile Payments: Apple Pay, Google Pay, and other digital wallet integrations streamline mobile checkout experiences.

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The Bottom Line

Shopify’s payment processing limitations don’t have to constrain your business growth. Each alternative offers unique advantages that might better align with your specific needs and budget.

Before selecting any platform, you need to understand your business model, transaction volume, and growth plans.

Take time to calculate your total processing costs across different platforms, including both gateway fees and platform charges. The savings from choosing the right alternative can fund marketing campaigns, inventory expansion, or other growth initiatives that drive your business forward.

Your choice impacts every transaction your business makes. Choose wisely, and you’ll build a foundation for sustainable, profitable growth in the competitive e-commerce landscape.

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