Best Shopify Payment Gateways in South Africa

Best Shopify Payment Gateways in South Africa

One of the drawbacks of setting up an ecommerce store on Shopify in South Africa is that Shopify Payments is not yet available in SA. That is why you will have to look at other options to allow you to accept payments online through your Shopify store.

Here's a comprehensive guide to our top Shopify payment gateways in South Africa.

Criteria to Look Out For in Best Payment Gateway in SA

When selecting the ideal payment gateway for your Shopify store, consider several essential criteria to ensure seamless transactions and customer satisfaction:

1. Transaction Costs

Analyze the fees charged per transaction by the bank and payment provider. Understanding the cost structure will help you determine how much of your sales revenue will go towards transaction fees. Look for transparent pricing models and compare transaction fees across different gateways to find the most cost-effective option for your business.

2. Merchant Account vs. No Merchant Account

 Decide whether to use a merchant account with your bank or a payment aggregator like PayFast or PayPal. A merchant account offers direct deposits into your business bank account and may provide better rates for high transaction volumes. However, setting up and maintaining a merchant account requires time and administrative effort. On the other hand, payment aggregators offer quick and easy setup with no need for a merchant account. Consider your business needs, transaction volume, and growth plans when choosing between the two options.

3. Customer Perception

Choose a payment gateway that instills trust in your customers. Online security and convenience are critical factors that influence customer purchasing decisions. Opt for well-known and secure payment gateways with user-friendly interfaces and reliable customer support. A seamless checkout experience enhances customer satisfaction and encourages repeat purchases.

4. Alternative Payment Methods

Evaluate whether offering alternative payment methods aligns with your customers' preferences and enhances their purchasing experience. Consider options such as credit card payments, split payments, instant EFT, and digital wallets. Providing multiple payment options caters to diverse customer needs and increases the likelihood of completing transactions. Assess the compatibility of each payment gateway with your ecommerce platform and integration requirements to ensure smooth payment processing.

Top 5 Best Payment Gateways in SA

Now, let's explore our top 5 Shopify payment gateways for South Africa ecommerce stores, along with their advantages and disadvantages:



Paystack is a leading payment gateway known for its reliability and security.

It provides a wide range of payment methods, making it convenient for both businesses and customers. Paystack's intuitive interface and robust fraud prevention measures make it a popular choice among online merchants in South Africa.

Key Features:

  • Receiving payments instantly after signing up
  • No integration or maintenance fees
  • Payments are automatically routed through the most optimal channels
  • Equipped with a combination of automated and manual fraud systems to protect against fraudulent transactions
  • Well-documented API (Application Programme Interface) allowing you to build a custom payment experience
  • Detailed reporting, alerts and exports, allowing you to analyze your business’ performance
  • Receive your money in your account 24 hours after payment is made
  • Accepts international customers
  • 24/7 customer support
  • No redirects
  • Automatic error resolution, in the event that a transaction fails


Local Transactions

2.9% + ZAR 1 (excluding VAT)

  • ZAR 1 fee waived for transactions less than ZAR 10
  • EFT transactions are charged at 2% with no flat fee
  • No upfront or monthly fees
  • All payouts are free

International Transactions

3.1% + ZAR 1 (excluding VAT)

Transfer Fees

ZAR 3 per transfer (failed or successful)

Supported platforms: WordPress, Shopify,, Opencart, Magento, PrestaShop

Squarespace and Joomla.

Available Payment options: Apple Pay, Visa QR, Mobile Money, POS, USSD, Bank Transfer, Bank Account and Card.

Peach Payments

Peach Payments

Peach Payments is a trusted payment gateway that specializes in providing comprehensive online payment solutions for businesses. With advanced safety features and fraud prevention measures, Peach Payments ensures secure transactions and seamless checkout experiences for customers.

Key Features:

  • 200 transactions per second with enterprise-grade bank-enabled security
  • Automated failover solution
  • Transactions can be switched to different banks based on card brand or volume
  • PCI/DSS Level 1 certified to reduce payment card fraud
  • Automated reconciliation templates that integrate easily with ERP system for seamless reporting




Growth Plan

The plan for SME


+R1.50 per txn (ex VAT)

  • No monthly fees or setup fees
  • Easy plugins to start your new store
  • 365 day phone & email support
  • Free, automated daily settlements
  • Accept local & international cards, EFT, Payflex, Mobicred

Enterprise Plan

Advanced Features


volume-based rates

  • For businesses that transact over R300,000 per month
  • Free, automated daily settlements
  • Dedicated Account Manager with daily priority support
  • API & SDK integrations, Magento plugins
  • Subscription and one-click checkout

Supported Platforms: WooCommerce, Shopify, Wix, Ecwid, Opencart, Magento, Gravity Forms, nopCommerce and Xero.

Available Payment options: Card, Pay by Bank, Scan to Pay, 1Voucher, Payflex and Mobicred.



With PayJustNow businesses can enhance customer affordability and increase sales by offering convenient payment solutions. The platform's user-friendly interface and transparent pricing make it an attractive choice for Shopify merchants in South Africa.

Key Features:

  • Buy now, pay later. PayJustNow pays the merchant at the time of transaction and the customer pays The PayJustNow system can determine shopper affordability, schedules automated deductions from the shopper’s selected debit or credit card and sends reminders to make sure they don’t miss payments.
  • PCI DSS complaint 

Available payment options: Visa and MasterCard debit or a credit card issued in South Africa.



Offering a user-friendly and secure platform for processing credit card payments online, Yoco boasts no minimum or monthly fees. Its simplicity of setup and extensive support for South African businesses make it an appealing choice for Shopify store owners.

Key Features:

  • Seamless setup, it takes just 5 minutes to create your Yoco profile and link it to your store
  • Yoco Gateway maintains industry-leading uptime, including real-time fraud monitoring
  • Flexible pricing for local transactions with no recurring fees
  • Yoco app allows you to manage products and track sales
  • Fast and flexible funding for qualifying Yoco customers
  • Yoco portal allows you to track your sales trends, staff performance, change your business info
  • Yoco Card machine allows you to connect your online and in-person sales




Core pricing

Less than R200 000 in transactions


*For local in-person rates

Excluding tax

  • Support 7 days a week
  • Connectivity fee is R49/month
  • Payout time of 1-2 business days
  • Payout fee is ncluded

Pro pricing

More than R200 000 in transactions


  • Dedicated Support 7 days a week
  • Connectivity fee is Included
  • Payout time of 1-2 business days
  • Payout fee included
  • Premium Device discounts

Supported Platforms: Shopify, WooCommerce, Shopstar, Wix and custom sites.

Available payment options: Visa, Mastercard, American Express, Apple Pay and Instant EFT.



Enabling customers to shop now and pay later with interest-free installment options, Payflex is an excellent solution for increasing order value and customer convenience, making it a valuable addition to any Shopify store catering to budget-conscious shoppers.

Key Features:

  • Available for online and in-person sales
  • Provide shoppers with flexible funding, paying the merchant upfront for purchases, while giving the shopper 6 weeks to pay – at 0% interest.
  • Seamless integration of payment gateway into your online store, or enable shoppers to pay via the Payflex app in-store.
  • Payflex offers two payment products that can be integrated online or in-store, Pay Now or Pay Later 
  • No additional charge your for setting up Payflex online or in-store

Pricing & Fees:

  • Payflex offers a simple fee structure with no fees for failed payments or authorisations.
  • Payflex charges a monthly nominal service fee (subscription) and a fee per successful transaction.
  • Further details on costs can be discussed with the Payflex sales team. 

Supported Platforms: Shopify, Wix, WooCommerce, Oppty, Opencart, Magento, PrestaShop, nopCommerce, CustomCMS, Storefront, Shopstar and API integration for custom-built websites.

Available Payment Options: Visa, Mastercard and American Express (Debit, Credit or Cheque).

Comparing Payment Gateways

Payment Gateway

Transaction Costs

Merchant Account

Customer Perception

Alternative Payment Methods


Transparent pricing with competitive rates

No merchant account required

Trusted by over 60,000 businesses

Offers flexible payment options including split payments

Peach Payments

Transaction fees starting at 2.95% + R1.50 per transaction

Offers merchant account options

Well-established player with over R1 billion processed monthly

Provides subscription billing and recurring payment options


Transparent pricing with no hidden fees

No merchant account required

High customer satisfaction with convenient payment options

Allows customers to split payments over three months with 0% interest


Transaction fees starting at 2.95%

No merchant account required

Trusted brand with over 200,000 businesses served

Offers seamless integration with various eCommerce platforms


Transaction fees undisclosed

No merchant account required

Increasing popularity with interest-free installment options

Allows customers to pay in four installments over six weeks with 0% interest

This comparison table provides a snapshot of the key features and benefits offered by each payment gateway in reference to the criteria to look out for when choosing a payment gateway.

Choosing The Right Gateway for Shopify

Selecting the right payment gateway is crucial for the success of your Shopify store in South Africa.

Consider factors such as transaction costs, merchant account requirements, customer perception, and alternative payment methods when evaluating payment gateways.

By choosing a reliable and secure payment gateway that meets your business needs, you can ensure seamless transactions and enhance customer satisfaction.

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