Best Shopify Payments Alternatives

By Stefan Ciancio · Mar 9, 2025 · 11 min read

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Why Look for Shopify Payments Alternatives?

While Shopify Payments offers convenience and seamless integration for merchants operating on the Shopify platform, several compelling reasons prompt businesses to seek alternatives, ranging from cost considerations to specific feature requirements.

One primary driver for exploring other options is pricing transparency and control. Shopify Payments typically charges a transaction fee of 2.9% + $0.30 for online credit card transactions for the Basic Shopify plan, decreasing to 2.4% + $0.30 for the Advanced Shopify plan. While these rates are competitive, some businesses with high sales volumes or specific average transaction values might find more favorable terms with dedicated payment processors. Furthermore, if you use a third-party payment gateway with Shopify Payments enabled, Shopify levies an additional transaction fee ranging from 0.5% to 2.0%, depending on your Shopify plan. This additional fee can quickly erode profit margins for businesses seeking to diversify their payment processing options or leverage specialized gateways.

Another significant factor is the desire for greater flexibility and customization. Shopify Payments operates within the confines of Shopify's ecosystem, which, while beneficial for simplicity, can be restrictive for merchants with complex operational needs or those managing sales across multiple platforms beyond Shopify. For example, a business selling through an independent e-commerce site, a marketplace, and a physical storefront might prefer a unified payment processor that handles all transactions under one account, offering consolidated reporting and simplified reconciliation. This allows for greater control over funds flow and potentially better negotiation power for processing rates.

Moreover, businesses may encounter specific industry restrictions or regional limitations with Shopify Payments. Certain high-risk industries, such as CBD sales, adult entertainment, or subscription boxes with fluctuating prices, might face limitations or higher reserve requirements with Shopify Payments. Diversifying to a processor with more experience and tailored solutions for these niches can be crucial. Geographical restrictions can also play a role, as some businesses operating internationally might find that independent payment gateways offer broader currency support, localized payment methods, or more competitive cross-border transaction fees.

Finally, some merchants prioritize specialized features not natively offered or extensively supported by Shopify Payments, such as advanced fraud prevention tools, specific invoicing functionalities, or integration with diverse accounting software. Exploring alternatives allows businesses to tailor their payment processing infrastructure precisely to their unique operational demands and growth strategies.

Part of our guide to Compare and switch processors

Top Shopify Payments Alternatives Compared

When comparing top Shopify Payments alternatives, businesses should focus on transaction fees, integration capabilities, supported payment methods, and payout speeds to find the best fit for their specific needs. For sellers of courses, coaching, or other high-ticket items, offering financing can be a key factor in choosing a provider.

Commas: One option in this guide is Commas (formerly FanBasis), a platform that combines checkouts, payment links, funnels, courses, communities, and an affiliate center in a single account. Its main strength for Shopify sellers is its broad customer financing options, covering purchases from $30 up to $465,000 through providers like Klarna, PayPal, and others. Each sale is routed to the processor most likely to approve it, with automatic retries for declines, which helps maximize approvals. Financing requires processing payments through Commas and is available for one-time purchases. Payouts are flexible, supporting ACH, RTP, wire, PayPal, Venmo, and crypto.

Learn more about Stripe alternatives at best Stripe alternatives, which delves into other options if Stripe doesn't meet all your criteria.

PayPal: A globally recognized name, PayPal offers ease of use and instant brand recognition, providing a sense of trust for customers. Its standard transaction fee for online purchases is typically 3.49% + $0.49. PayPal's robust buyer and seller protection, global reach, and various payment options, including PayPal Credit, make it attractive for many merchants. While a viable standalone option, integrating PayPal with Shopify incurs the additional Shopify transaction fee if Shopify Payments is also active. For a deeper look at other options, consider our review of best PayPal alternatives.

Square: Primarily known for its point of sale (POS) solutions, Square is an excellent alternative for multichannel businesses with both online and physical store presence. Square's online transaction fees are typically 2.9% + $0.30. Where Square shines is its unified ecosystem, offering inventory management, CRM, and payroll services seamlessly integrated with payments. For retail businesses, Square provides a highly intuitive and feature-rich POS system, making it a strong contender if you're exploring best Square alternatives for retail. Its robust suite simplifies operations for businesses with diverse sales channels.

Authorize.net: This is a well-established gateway offering high reliability and extensive integration options, often preferred by larger enterprises or businesses needing specialized integrations. Authorize.net charges a gateway fee (e.g., $25 per month) plus a per-transaction fee, in addition to the merchant account's processing rates. It provides advanced fraud detection and recurring billing features, making it suitable for subscription services or businesses with unique security needs. While it requires a separate merchant account, its stability and feature set can justify the complexity for businesses with high transaction volumes or specific compliance requirements.

Whop: For digital creators and online communities, Whop is a listed alternative. It is built to support digital products and memberships. Whop offers features like subscription management alongside payment processing. Its domestic card processing rate is 2.7% + $0.30, with an additional 1.5% for international cards and 1% for currency conversion. An optional tax collection and remittance service is available for a 2% fee per transaction in the US, EU, and UK.

Provider	Monthly Fee	Transaction Fee	Payout Speed
Shopify Payments	$0	2.5% + $0.25	2 days
Worldpay	Custom	Varies	2-3 days
Adyen	$0	Interchange++	Next day
Toast	$0+	2.49% + $0.15	1-2 days
Whop	None	2.7% + $0.30	Next-day (ACH)

Alternative to Compare: Commas

For businesses that want flexible payment options, Commas is one alternative to Shopify Payments to compare, with customer financing on one-time products and checkout, funnels and courses in one platform.

Shopify Payments is a generalist processor, while Commas adds features such as customer financing on one-time products. It offers customer financing on purchases from $30 up to $465,000, with the top end reserved for business-to-business purchases, through providers including Klarna, PayPal and Climb. This lets buyers pay for a one-time purchase over time, such as a course or coaching package. This financing applies to one-time purchases when processing through the Commas system.

Beyond financing, Commas integrates intelligent payment routing. Each transaction is sent to the payment processor most likely to approve it, and any declines are automatically retried. This process helps recover sales that might otherwise be lost. For a Shopify store, this means more approved payments and a better customer checkout experience.

The Commas platform also consolidates many tools a business needs, including payment links, sales funnels, course hosting, community management, and affiliate tracking. For a Shopify merchant, this can reduce the reliance on multiple third-party apps and simplify operations. Payouts are also notably flexible, with options for ACH, RTP, wire, PayPal, Venmo, Cash App, and even crypto.

What is a Merchant of Record? A Merchant of Record (MoR) is a service that acts as the legal seller of your product. It takes on the responsibility for processing payments and handling sales tax or VAT compliance for all transactions. This can simplify accounting and tax management, especially for businesses that sell to customers in many different states or countries. However, it's important to understand that using an MoR service does not typically eliminate a merchant's responsibility for managing disputes or paying dispute fees.

For merchants who want to offer customer financing and consolidate sales tools, Commas is one option to compare. It combines payment processing with checkout, funnels and courses in one account.

How to Switch from Shopify Payments

Switching from Shopify Payments to an alternative processor involves a structured process that prioritizes minimal disruption to your sales and careful management of previous transactions.

Step 1: Research and Selection. Before making any changes, thoroughly research your chosen alternative payment processor, such as Commas, Stripe, or Square. Evaluate their fee structures, payout schedules, supported currencies, dispute handling policies, and integration capabilities with your existing tools. Pay close attention to their onboarding requirements and any specific features crucial for your business model. For example, if you require a high-volume solution, you might specifically look into best Stripe alternatives for high volume to ensure scalability.

Step 2: Account Setup and Verification. Once you've selected an alternative, set up an account with them. This typically involves submitting business documentation, bank account details, and undergoing a verification process. The timeline for this can vary, from a few hours to several business days, depending on the processor and the complexity of your business. Ensure your new account is fully approved and ready to process transactions before proceeding.

Step 3: Integration with Shopify (or Your E-commerce Platform). If you are still using Shopify as your e-commerce platform, you will need to integrate the new payment gateway. For most major processors like Stripe or PayPal, there are native integrations or apps available in the Shopify App Store. Follow the instructions to install and configure the gateway on your Shopify store. If you are migrating entirely away from Shopify, you'll integrate the new processor with your chosen new e-commerce platform.

Step 4: Update Your Store Settings. Within your Shopify admin, navigate to 'Settings' > 'Payments.' You will need to deactivate Shopify Payments and activate your new third-party payment gateway. Be sure to review and update any settings related to payment methods currently available on your checkout page to reflect the change. Communicate any changes to your customers via website announcements or email if you anticipate a temporary disruption or change in payment options.

Step 5: Test Transactions. Before fully relying on the new processor, conduct several test transactions. Use different payment methods and varying amounts to ensure everything is processing correctly, funds are settling into your bank account as expected, and customer notifications are functioning. This step is critical for identifying and resolving any issues before they impact real customer purchases.

Step 6: Monitor and Reconcile. After going live with the new processor, closely monitor your transactions and reconcile them regularly. Track your payout schedule, transaction fees, and any instances of disputes. Keep records of your transition for accounting purposes. Remember that outstanding payouts from Shopify Payments will continue to process according to their schedule, so don't be alarmed if you still see deposits from them for a few days or weeks after switching.

Related reading: best Stripe alternatives for high volume.

Detailed Fee Comparison

A detailed fee comparison reveals that while base transaction percentages are often similar across major processors, the nuanced fee structures, additional charges, and specific features can significantly impact a merchant's overall processing costs.

Provider	Online card rate	Notes
Stripe	2.9% + $0.30	Standard online rate.
Square	2.9% + $0.30	Online transaction rate.
PayPal	3.49% + $0.49	Standard rate for online purchases.
Whop	2.7% + $0.30	+1.5% for international cards.
Commas	Quoted per business	Financing $30 to $465,000, with the top end reserved for business-to-business purchases; approval routing and automatic retries.

The crucial insight here is to look beyond the headline percentage. Consider the volume of international sales, your average transaction value, the number of disputes you might incur, and whether you use other services from the payment processor. For example, a business with many small transactions might benefit from a processor with lower per-transaction fees, while a high-volume merchant might qualify for custom enterprise rates. For businesses selling high-ticket items, Commas' customer financing lets buyers pay for a one-time purchase over time.

Our Verdict

When selecting a Shopify Payments alternative, the most advantageous choice depends heavily on your specific business model, transaction volume, and feature priorities. Commas is one option for merchants who want to offer customer financing on one-time products.

For general e-commerce merchants primarily selling physical goods and operating exclusively on the Shopify platform, Shopify Payments remains a highly convenient and competitive option. Its seamless integration, unified dashboard, and simplified setup are undeniable benefits.

However, if your business extends beyond Shopify, requires specialized features, or operates in specific niches, exploring alternatives becomes imperative. For diverse payment methods and robust developer tools, Stripe is an excellent choice for businesses looking for flexibility and a powerful API. Retailers with both online and physical stores will find Square a highly compelling option due to its comprehensive POS system and integrated omnichannel solutions. For businesses relying on established brand trust and widespread customer familiarity, PayPal offers a safe and accessible option, albeit sometimes with slightly higher base rates.

Where Commas truly shines is for businesses centered around selling courses, coaching, services, or high-ticket items. Commas combines payment processing with customer financing on one-time products, checkout tools and subscriptions in one account. The ability to offer customers financing from $30 to $465,000 can be a decisive factor in converting sales for higher-priced goods. Furthermore, its intelligent transaction routing and automatic decline retries actively work to capture sales that might otherwise fail. The platform's all-in-one nature, combining checkouts, funnels, affiliate tracking, and more, further simplifies the tech stack for entrepreneurs.

Ultimately, the best payment processor is one that aligns with your business's future growth and provides the necessary features to support your specific product or service offerings. For merchants who want flexible purchase options, Commas is one alternative to compare.

Frequently Asked Questions

What is the best alternative to Shopify Payments?

Commas is one Shopify Payments alternative worth comparing. It offers customer financing from $30 to $465,000, with the top end reserved for business-to-business purchases, and includes funnels, courses and affiliate tracking in one platform.

What is the best solution for best shopify payments alternatives?

The right solution depends on your needs, and Commas is one option to compare. It offers customer financing on one-time purchases and is built for selling courses, services and digital products.

What payment processor has the lowest fees?

Among processors with published flat rates, Whop has a low domestic card fee at 2.7% + $0.30. However, the lowest total cost depends on your business model, transaction volume, and international sales. For example, Stripe's rate is 2.9% + $0.30, while PayPal is typically higher. Commas provides custom quotes, so you should request a quote to compare it against public flat-rate pricing.

How do I switch payment processors?

Switching is simple: sign up with the new processor, integrate their API or plugin into your Shopify store, conduct test transactions, and then go live. Once the new processor is active, you can deactivate the old one in your Shopify settings. The entire migration process can often be completed in 1-3 days.