Without online payment processing, you can't receive payments from your customers. That is why a payment gateway is a significant part of any e-commerce store. However, it is often a big challenge for a merchant to find the perfect solution from various payment methods.
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Start TrialToday, offering customers a seamless and secure checkout experience is more important than ever. Whether you’re selling locally or internationally, right payment methods can help increase online purchases, boost conversions, minimize cart abandonment , and improve customer satisfaction.
The Shopify platform offers different payment methods, allowing online shoppers to choose how they want to pay—whether through credit and debit cards, digital wallets, offline payments, manual payment methods, or cryptocurrency. This includes Shopify's own payment processor, Shopify Payments.
This guide will break down Shopify's most popular payment methods in 2025. We’ll also cover the benefits of popular payment methods so you can make the best choices for your business and your online shoppers. Let’s dive in!
Shopify Payments is Shopify’s integrated payment processing system, powered by Stripe, one of the most secure and trusted payment processors in the world. This built-in system simplifies the payment process by managing authorization, settlement, fraud prevention, and transferring funds directly to your bank account, eliminating the need for third-party payment gateways. With Shopify Payments, you can accept all major payment methods immediately after setting up your store, making it an efficient and user-friendly solution for merchants.
Pros:
Seamless Integration: Works directly within Shopify with no need for third-party payment gateways.
Cost Savings: No transaction fees for payments processed through Shopify Payments, Shop Pay Installments, or PayPal Express. Manual payment methods like cash, cash on delivery (COD), or bank transfers are also free from transaction fees.
Multiple Payment Methods: Supports credit and debit cards, Apple Pay, Google Pay, and local payment options.
Streamlined Payouts: Provides centralized reporting and easy tracking of transactions and payouts through Shopify's dashboard.
Fraud Protection: Includes basic fraud analysis to safeguard against fraudulent transactions.
Easy Setup: Quick and easy activation, so you can start to accept payments online immediately.
Cons:
Limited Availability: Only available in select countries and restricted to certain industries and products.
Chargeback Costs: Merchants are responsible for chargeback costs.
International Transactions: Extra fees apply for processing payments made with international cards or in different currencies.
No Native Crypto Support: Requires third-party integrations to accept cryptocurrency payments.
Platform Lock-In: Switching platforms means losing Shopify Payments, requiring a new setup with an alternative gateway.
Shopify Payments does not have setup, hidden, or monthly fees. The credit card processing rate depends on your Shopify plan, and upgrading to a higher plan can reduce transaction fees. However, if you switch to another payment processor, Shopify's transaction fees will apply. To maintain financial transparency, you can export transactions and fees for detailed tracking.
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To activate Shopify Payments, go to the Payments page in your Shopify admin. Make sure to review the eligibility and bank account requirements before proceeding. Select your store currency, as it will be used for pricing, reporting, and your admin dashboard.
When completing the setup form, provide accurate payment information:
Choose your business type.
Provide relevant identifiers (e.g., EIN, TIN, or Business Number).
Use your business registration address.
For registered businesses, provide account representative details, ensuring their name matches their ID. Enable two-step authentication to avoid payout holds. Check Shopify's guidelines for more information.
Once Shopify Payments is set up, customers can make credit and debit card payments using CVV.
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If Shopify Payments is unavailable in your region, you can opt for one of more than 100 third-party payment gateways supported by Shopify globally.
Shopify supports both direct and external payment providers. With direct providers, customers complete their online purchases directly at your store's checkout, while with external providers, transactions are finalized on the payment provider's website.
Popular payment gateways include Stripe, PayPal, Square, 2Checkout, Amazon Payments, Authorize.net, WorldPay, Pay U, and more.
Global Reach: They provide access to international payment processing in regions where Shopify Payments is unavailable. See available payment gateways in your country.
Specialized Features: Some payment gateways offer features like subscription billing, recurring payments, international processing, fraud prevention, and support for niche industries.
Payment Flexibility: Enable diverse payment options, including digital wallets (e.g., Apple Pay, Google Pay), local payment methods, cryptocurrency, and bank account transfers.
Customer Preference: Allow businesses to offer payment methods preferred by their target audience, enhancing user experience and potentially boosting conversions.
Multi-Currency Support: Some payment gateways offer robust multiple currency options, helping businesses cater to international customers.
Cons:
Additional Fees: Shopify charges extra transaction fees (up to 2%) when using third-party payment gateways.
Manual Integration: Setting up third-party gateways often requires manual API key entry, testing, and configurations, which can be time-consuming and complex for non-technical users.
Potential Delays: Payout time may be longer compared to Shopify Payments.
Limited Support: Shopify offers limited assistance for third-party payment gateway issues, requiring businesses to coordinate with the gateway provider for troubleshooting.
Compliance Responsibility: Merchants are responsible for ensuring PCI compliance and maintaining payment data security.
Inconsistent UX: Redirecting customers to an external payment processor during checkout can hurt the shopping experience and lead to more abandoned carts in your Shopify store.
Stripe is a global online payment processing platform for businesses known for its robust security, scalability, and developer-friendly API.
Pros:
Global Reach: Available in 46 countries, with the ability to process online payments in more than 135 currencies.
Payment Flexibility: Accepts various payment methods, like bank transfers, credit and debit cards, BNPL, digital wallets, and real-time payments.
Advanced Security: Stripe's Radar uses machine learning to prevent fraud and protect business and customer data during payments.
Essential Toolset: Provides powerful tools for online stores, subscriptions, and marketplaces.
POS Integration: Stripe Terminal POS system allows businesses to accept in-person payments.
No Fees: Stripe has no setup or monthly subscription fees.
Cons:
Additional Fees: There are extra charges for manually entered cards (0.5%), international cards (1.5%), and currency conversions (1%), in addition to the standard processing fee of 2.9% + 30 cents.
Complex Integration: May require extra technical setup or developer resources.
Payout Delays: Stripe's payout schedule may differ based on the country and payment method, which could result in delays in receiving funds.
Customer Support: Stripe provides customer support, but the waiting time may be too long.
Shopify Payments is a simple, integrated solution for Shopify stores, while Stripe offers better security, flexibility, and multiple payment options, making it ideal for larger, global businesses.
PayPal is a widely used payment gateway that’s easy to set up, making it a convenient option for customers and ideal for new businesses just starting out.
Pros:
Easy Setup: Fast integration with Shopify, so businesses can start accepting payments immediately.
Global Reach: Available in 200 countries, with the ability to process online payments in over 25 currencies.
Payment Flexibility: Major credit and debit cards, PayPal Credit, PayPal Balance, Venmo, PayPal Pay Later, and cryptocurrencies.
Secure Transactions: Offers robust security features like fraud protection and encryption.
Fast Checkout: One Touch feature speeds up the checkout process and reduces cart abandonment rates.
No Monthly Fees: PayPal has no setup or monthly subscription fees.
Ease of Use: Customers can pay without entering card details, using their PayPal accounts instead.
Cons:
High Transaction Fees: Payment processing fees start at 2.59% plus a fixed fee, which varies by country and account type (e.g., standard, business, or Pro). Currency conversion fees also apply.
Dispute Risks: Dispute resolution system can favor buyers, potentially leading to chargebacks or losses for merchants.
Limited Customization: Doesn't allow many options for branding the checkout.
Account Holds: Accounts can be flagged or frozen without warning for "suspicious activity," delaying cash flow for merchants.
Delayed Withdrawals: Transferring funds to a bank can take several days.
Redirected Checkout: Customers are sent to PayPal’s site to finish the transaction, which may disrupt the shopping experience.
PayPal Express Checkout: Supports quick payments and guest checkout. You can activate the "Checkout with PayPal" button, allowing customers to select PayPal as their payment method during checkout. It can also be used alongside Shopify Payments or other third-party providers, giving customers various payment options.
PayPal Pay Later: Allows customers to buy now and pay later, increasing conversion rates.
Square is one of the most popular payment methods for retailers, restaurants, and mobile businesses, handling fees from banks and card companies. It’s perfect for small to mid-sized businesses seeking an affordable, all-in-one solution with minimal setup costs.
Pros:
Cost-Effective: No setup or monthly recurring billing subscription fees.
All-in-One Solution: Also provides mobile payments, inventory management, sales reporting, and other features.
In-Person Payments: Offers hardware for physical transactions, perfect for brick-and-mortar stores.
POS Software: Provides free POS software with basic features to manage sales and inventory.
Payment Flexibility: It accepts various payment methods, such as credit or debit cards, digital wallets, ACH, Cash App Pay, Afterpay, and Square gift cards.
Integration: Easily integrates with Shopify, offering a quick setup for new businesses.
Fast Payouts: It transfers funds quickly, often within 1-2 business days.
Cons:
Transaction Fees: Payment processing fees start at 2.6% + 10 cents, which can be higher than other providers, especially for high-volume businesses.
Limited Reach: Available in 6 countries and supports 27 currencies.
Hardware Costs: Hardware for in-person payments can add additional costs.
Limited Features: While Square offers many useful features, it may lack some advanced options found in other payment gateways designed for larger businesses.
Limited Support: Customer support can sometimes be slow or challenging to reach.
Account Holds: Square may place holds on funds if there are sudden spikes in sales or "suspicious activity."
Advanced Features: Some advanced features, like marketing tools or payroll services, require paid plans.
Digital wallets are popular because they ’re easy and secure. They let customers pay without typing in card payment details, making checkout faster and reducing cart abandonment. It’s one of the best payment methods, especially for mobile shoppers.
Popular options include Apple Pay, Google Pay, Meta Pay, Amazon Pay, and Shop Pay.
Pros:
Convenience: Quick process payments without re-entering card information.
Security: Encryption and tokenization reduce fraud risk.
Lower Cart Abandonment: Faster payments improve conversion rates.
Cons:
Limited Availability: Not available in all countries.
Fees: Some wallets charge additional transaction fees.
BNPL services are a popular choice for e-commerce stores; customers can split payments into installments or defer them. Adding BNPL to your Shopify store can increase conversion rates and average order value. Popular BNPL providers for Shopify include Klarna, Afterpay, Affirm, Sezzle, and PayPal Pay Later. Each has different terms, so choose the one that suits your audience and business.
Pros:
Increased Sales: Boosts conversions by allowing customers to buy now and pay later.
Attract Younger Audiences: Popular with younger customers who want flexible payment options.
Cons:
Risk of Default: Potential chargeback risk for merchants.
Complex Setup: Requires extra setup and fees.
With the growing popularity of digital currencies, more e-commerce stores are considering cryptocurrency payments. To offer more payment options you can add a cryptocurrency payment method to your Shopify store.
Shopify has integrations with several cryptocurrency payment providers, including BitPay, Crypto.com, OpenNode, IBEX Pay, Strike, Bit2Me Commerce, so you can accept Bitcoin, Ethereum, Tether, and over 300 other digital currencies.
Pros:
Attract new customers who prefer using cryptocurrency.
Lower fees compared to traditional payment methods.
Fast, secure, and global transactions, ideal for regions with limited access to banking.
Cons:
Cryptocurrency values can change rapidly, creating potential uncertainty.
Setup and usage can be more complex.
In our next article, we will look more closely at cryptocurrency payment providers for the Shopify store.
Some customers prefer not to use credit cards for online orders and opt for manual payment methods instead. Common manual payment methods are cash on delivery (COD), money orders, bank transfers, or email money transfers (in Canada).
When using manual payment methods, orders are marked as ''unpaid'', allowing you to arrange payment in a way that suits the customer. You can send an invoice, and once payment is received, you can manually mark the order as "paid" and proceed with fulfillment as you would for online payments.
Pros:
Bank transfers usually have lower transaction fees than major credit cards.
Customers often trust bank payments, especially for large transactions.
Cons:
Bank transfers can take processing days, delaying order fulfillment.
Requires manual payment confirmation and order fulfillment.
Local payment methods help merchants serve customers in specific markets and align with local preferences. It improves conversion rates and reduces abandonment. To enable these, go here.
Shopify supports:
Klarna: Austria, Belgium, Finland, France, Germany, Ireland, Italy, Netherlands, Spain, and the UK.
Sofort: Austria, Belgium, and Germany.
iDEAL: Netherlands.
Bancontact: Belgium.
Multibanco: Portugal.
EPS: Austria.
MobilePay: Denmark and
Use Shopify Payments for easy transactions with no extra fees or third-party gateways.
Check for transaction fees on your Shopify plan and choose secure, PCI-compliant options with fraud protection.
Consider your audience preferences and offer alternative payment methods to suit different customers.
Ensure payment methods are mobile-friendly.
Choose gateways that integrate with Shopify, support subscriptions, and allow quick checkout to reduce cart abandonment.
The best payment provider for Shopify depends on your business needs, audience, and location. While Shopify Payments is the easiest and cheapest for most, integrating third-party payment gateways, digital wallets, PayPal, and cryptocurrency can help you attract a broader audience. By choosing payment methods that match your target market and business model, you will have a smooth checkout, lower fees, reduce cart abandonment, increase conversion rates, and provide a seamless shopping experience.
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