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  5. 6 Best E-commerce Credit Card Processing Companies [2024]

6 Best E-commerce Credit Card Processing Companies [2024]

Andrés Gánem Andrés GánemFinance Specialist April 05, 2024
April 05, 2024
Unless you plan on receiving cash via messenger pigeon, credit card processing is crucial to your online business. It’s not just about accepting credit cards, either. You can put all the time in the world into perfecting your products and web design, but it will largely be in vain if your payment method is inconvenient. Without an easy way to pay, many customers will simply bounce to another site.

A good payment processor, then, should offer a frictionless payment experience for your customers. The best processors, though, will also make your life easier. Sadly, tons of credit card processors out there are riddled with hidden fees, have ridiculous markups, or just don’t provide the tools that an e-commerce business needs to thrive.

That’s where I come in. After scouring hundreds of reviews and carefully researching what all of the major payment processors offer, I found the very best credit card processors for e-commerce. My top recommendation for e-commerce businesses is Leaders Merchant Services (LMS). You’ll get a payment gateway, virtual terminal, free POS equipment, shopping cart integration, and some of the lowest rates in the industry.

Keep on reading to see our other top recommendations for e-commerce payment processing.

Short on Time? These Are the Best Credit Card Processors for E-commerce in 2024

  1. Expert’s Choice
    LMS_Monogram Leaders Merchant Services
    Leaders Merchant Services is a popular choice with our readers
    The best processor for negotiating the right deal for your online business.
  2. logopayarc PAYARC Advanced tools for e-commerce and custom plans with 0% markup on transactions.
  3. promerchant-logo ProMerchant Impressive e-commerce features and integrations backed by powerful fraud protection tools.

What We Look For in the Best Credit Card Processing Companies for E-commerce

Besides offering a high-quality service in general, the processors on this list had to meet meet the following criteria to be considered an ideal fit for e-commerce businesses:
  • Shopping cart integrations. There is (practically) no way to create an online store without shopping cart features. The processors on this list offer shopping cart integrations with the most popular website builders and e-commerce platforms. It’s also preferable that they include APIs to give web developers even greater flexibility.
  • High security standards. E-commerce businesses are more likely to be deemed high-risk because card-not-present transactions are vulnerable to a slew of security threats. I only included processors that meet the highest security standards for you and your customers. Double points if they offer PCI-compliance assistance.
  • Fair pricing. No business can afford to throw away money on subpar features. I only included processors that offer benefits and features that justify their rates.
  • Ease of setup and use. E-commerce businesses can’t afford to wait weeks or have to jump through an endless procession of hoops to set up credit card processing. The processors on this list offer quick and simple onboarding and an easy-to-use service.

Leaders Merchant Services (LMS) is a great option if you process both in-person and e-commerce transactions. For card-present payments, they offer the full range of Clover’s products and a couple of more traditional EMV readers. You’ll also get the Authorize.net gateway and CartManager shopping cart integration for e-commerce.

That might not sound like a lot for businesses that operate mainly (or only) online, but the truth is that a payment gateway and shopping cart integration will be enough for most small businesses. What’s more, CartManager and Authorize.net are some of the most popular and trustworthy e-commerce apps available.

This isn’t LMS’s biggest advantage, though. The reason it’s so high on this list is that LMS gives you plenty of room to negotiate what fees you’ll pay on your plan. When you sign up with LMS, you’re able – even encouraged – to negotiate for the best possible price based on the unique characteristics of your business. This flexibility means that LMS can give you the best deal possible, freeing up extra cash in your budget that you can invest back into your business.

Features and Benefits

  • Cash advance options. If your business is just getting off the ground, LMS offers merchant cash advances – a type of loan where you receive a set amount of cash that you pay back via a small commission on your credit card sales.
  • Instant Accept. If you use QuickBooks for your bookkeeping, LMS offers Instant Accept as a paid add-on. This lets you receive custom invoices directly from your QuickBooks dashboard and automatically updates your info accordingly.
  • Personalized plans. When you sign up, LMS offers tools specific to your industry, such as gift card programs and subscription services.
  • Outstanding POS variety. This will matter less if you conduct your business solely online, but hybrid businesses will appreciate the wide range of point of sale devices LMS has available.
Discover more features in our expert Leaders Merchant Services review.

Payment Gateways Authorize.net
PCI assistance
Customer analytics and reporting tools Yes, via Authorize.net
Transaction fees on cheapest plan ~2% + 0¢
Monthly subscription on cheapest plan $9.00

Out of all the processors I researched, Stax offers one of the longest lists of specialized tools for e-commerce. The Stax gateway provides shopping cart integrations with popular platforms like Bigcommerce, WooCommerce, and SalesForce. It also offers analytics and reporting tools to help you track product performance, customer tendencies, and more.

Something else that impressed me is that Stax doesn’t charge a percentage markup on transactions. If your business is based in the US and you typically process a large volume of sales, Stax’s pricing model could save you up to 40% on your card processing bill.

Stax does charge a monthly fee that might be steep for some merchants. If you process less than $5,000 a month or your revenue mostly comes from a few costly orders, you’ll likely save money using a processor with an interchange-plus pricing model. Still, when it comes to helping online businesses thrive, Stax’s e-commerce tools are impressive.

Features and Benefits

  • Developer tools. If you’re a more tech-savvy merchant or you can afford to hire a professional developer, Stax’s easy-to-use API will let you create custom integrations, shopping carts, and more.
  • Dashboard software. Stax offers proprietary software for managing all your processing information from one place, making it one of the few payment processors providing this feature. With the Growth plan, you gain access to a straightforward dashboard to monitor your sales and obtain basic customer analytics. On the other hand, the Pro and Ultimate plans offer more advanced analytics capabilities.
  • Useful integrations. Stax offers integrations with a wide variety of business software to help you keep things running smoothly. These let you do things like sync with QuickBooks and automatically send important updates to your team via Slack.
  • Digital invoicing. Stax gives you the tools to create, customize, and keep track of digital invoices in real time. You can also set up recurring invoices, which are ideal if you offer subscriptions or ongoing services.
Check out our in-depth Stax review to learn more.

Payment Gateways Proprietary
PCI assistance Assistance dashboard and comprehensive resources
Customer analytics and reporting tools
  • Advanced analytics dashboard
  • Customer management software
  • Advanced reporting tools
Transaction fees on cheapest plan 0% + 10¢ (in-person)
Monthly subscription on cheapest plan $99.00
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3. PaymentCloud: Good Choice For Higher Risk E-commerce Businesses

If your business is in a higher-risk industry or you lack sufficient credit processing history to satisfy most payment processors’ underwriting, PaymentCloud is your ideal solution. It boasts a 98% approval rate, outstanding customer support, and a sophisticated suite of e-commerce features.

Once PaymentCloud approves your account, you can expect a same-day setup of e-commerce tools such as a virtual terminal and your choice of one or more payment gateways. While PaymentCloud offers plenty of integrations, its API is also easy to customize, making it simple to connect software you and your staff already use.

While PaymentCloud offers great value for high-risk businesses, it’s also suitable for all types of businesses regardless of risk level. Lower-risk merchants will benefit from its outstanding e-commerce features and will also enjoy reduced rates and monthly plans with no cancellation fees.

Features and Benefits

  • Business integrations. With more than 170 useful integrations you’re sure to find the perfect tool to help you grow and manage your business. PaymentCloud seamlessly integrates with e-commerce, shopping cart, marketing, and management tools.
  • Funding options. From bridge loans to business lines of credit, PaymentCloud has a quick and flexible option to meet the needs of your business. Funding can be available in as little as 24 hours.
  • Advanced fraud protection.PaymentCloud guards against data breaches and suspicious transactions with features like Address Verification Service (AVS), Card Verification Value (CVV), and complex machine learning algorithms. This ensures your customers’ data and your funds are safe and reduces the likelihood of chargebacks.
  • Payment methods. Your customers can pay by debit or credit card, cryptocurrency, e-check (ACH), and other MOTO (card not present) payment methods. With the Paysley app, they can also use their mobile phones for contactless payments by scanning a QR code or clicking on a text or email link.
Learn more about PaymentCloud in our expert review.

Payment Gateways Multiple payment gateways including Authorize.net, NMI, Braintree, and Cybersource (through integrations)
PCI assistance
Customer analytics and reporting tools
  • Customer management software (with integrations)
  • Inventory management (with integrations)
  • Analytics and reporting tool
Transaction fees on cheapest plan Around 2.1% + 15¢
Monthly subscription on cheapest plan $14.00

4. PAYARC: Custom Plans With Outstanding E-Commerce Tools

E-commerce merchants looking for a more personalized approach to their credit processing needs may want to explore PAYARC. Features and fees for both its competitively-priced membership and flat rate plans are tailored for each client. What’s more, with a membership plan, you’ll pay a 0% markup on all transactions.

Every plan includes PAYARC’s outstanding payment software that seamlessly integrates with your website or existing e-commerce platform. Built-in tools allow you to create and customize invoices, automate tax collection, adjust pricing based on purchase volume, and adjust billing to reflect discounts and promotions.

To take full advantage of what PAYARC offers, you can use its secure API to further personalize your dashboard and e-commerce features. While you’ll find step-by-step instructions in the developer’s guide to walk you through the setup process, PAYARC offers what few payment processors do: API onboarding for quick and easy setup.

Features and Benefits

  • Advanced business software. PAYARC offers impressive technology-driven features for managing your business, including built-in invoicing, data-driven reports, and real-time sales and payment tracking.
  • International e-commerce. Through its partnerships with global payment gateways, PAYARC allows you to market products and services to an international clientele. Your customers will have the option to pay in their own currency at checkout.
  • Convenient dashboard. From your PAYARC dashboard, you can access detailed reports and analytics to make data-backed decisions for your business. You can also manage sales, subscriptions, invoices, disputes, and more.
  • Security and risk monitoring. A suite of tools helps protect your business from cybercrime and fraud. These include limits/blocks on select countries and IP addresses, velocity filtering, tokenization, encryption, and AVS/CVV (address and zip code and security code) verification.
Read our expert PAYARC review for more details.

Payment Gateways
  • Proprietary payment gateway
  • Integration with Authorize.net gateway and several international payment gateways
PCI assistance Yes, with Control Scan integration (fees may apply)
Customer analytics and reporting tools
  • Advanced analytics dashboard
  • Customer management software
  • Advanced reporting tools
Transaction fees on cheapest plan 2.49% + 30¢ (in-person)
Monthly subscription on cheapest plan N/A

5. ProMerchant: Fast Setup and Affordable Pricing for Online Businesses

Whether your e-commerce business is new or established, you’ll appreciate ProMerchant’s affordable payment models, fast payout times, and e-commerce software. Another standout feature is the option for next-day funding, standard on every merchant account.

ProMerchant uses the well regarded Authorize.net payment gateway, which works with most popular e-commerce and business platforms like BigCommerce, Magento, and QuickBooks. It comes with fraud protection features, digital invoicing, and the ability to set up recurring payments for subscriptions or payment plans.

If you also have a brick-and-mortar location or sell at popups, events, and marketplaces, ProMerchant offers free Ingenico desk and Pax Mobile POS terminals.

While ProMerchant offers a lot, including excellent customer and technical support, the only way to get a sense of your true cost is to reach out to sales support for a quote. On the other hand, it doesn’t charge hidden fees and its customer reviews are overwhelmingly positive.

Features and Benefits

  • Advanced inventory management.  ProMerchant’s robust inventory management system helps ensure you maintain optimal stock levels so you never miss a sale. It includes real-time updates on stock levels, automated alerts for low inventory, and seamless integration with your suppliers.
  • AI-powered product recommendations. AI analyzes user behavior, purchase history, and browsing patterns to suggest personalized products to each visitor. This intelligent tool can enhance customer engagement and increase your site’s conversion rates.
  • Multi-channel selling. You can expand your market reach by listing your products across online marketplaces and social media platforms. A centralized dashboard lets you manage all your sales channels from one place.
  • One-page checkout. Streamline the checkout process with ProMerchant’s one-page checkout for a hassle-free shopping experience that increases customer satisfaction and reduces cart abandonment rates.
For more details, see our in-depth ProMerchant review.

Payment Gateways Authorize.net
PCI assistance No, but regular security scans and alerts
Customer analytics and reporting tools
  • Customer management software
  • QuickBooks sync (through integration)
  • Advanced reporting tools (through integration)
Transaction fees on cheapest plan 3% + 10¢ (credit)
Monthly subscription on cheapest plan $7.95

6. Flagship Merchant Services: Fast and Easy Set Up

On the surface, Flagship Merchant Services’ offering might seem pretty basic. Like some others on this list, Flagship offers reliable online payment processing via the Authorize.net gateway.  In addition, you’ll get a virtual terminal, subscription management tools, and a developer kit that’ll allow you to build custom integrations and shopping carts.

On top of that, Flagship stands out for its fast and easy application process. In some cases, you’ll be able to start processing payments as soon as a couple of hours after sign-up. Its pricing information could be clearer, and it doesn’t offer the most advanced analytic tools out there, but Flagship is the best option if you need to start processing online payments quickly.

Features and Benefits

  • Custom security restrictions. Besides the usual security features, Flagship allows you to set custom security restrictions like setting a maximum number of charges per card or even excluding specific IP addresses.
  • Loyalty program. Pirq powers an optional digital loyalty program that Flagship offers. This app-based loyalty scheme rewards customers for each in-store or online purchase when they scan the associated QR code. It’s a fantastic, cost-effective method to stimulate repeat business on your e-commerce store.
  • iAccess portal. When you set up a Flagship account, you also receive the iAccess software. iAccess allows you to create daily, weekly, and monthly processing activity reports. It also gives you access to custom analytics, such as comparing your sales performance to other businesses in your area.
  • Same-day funding. For a small fee, you can receive payouts within 12 hours of making a sale.
Read our expert Flagship Merchant Services review for more information.

Payment Gateways Authorize.net
PCI assistance No, but regular security scans and alerts
Customer analytics and reporting tools
  • Merchant console
  • iAccess Portal
Transaction fees on cheapest plan 1.58% + 19¢ (in person)
Monthly subscription on cheapest plan $7.95

Make the Most Out of Your Business With the Right Processor

A great e-commerce credit card processor should do much more than just process credit cards. The right processor will offer you the tools to keep your data secure, save you money, and expand your business (and process credit cards – that’s pretty important too).

If your business takes both in-person and online payments, Leaders Merchant Services provides a great service at a negotiable price.

If you’re looking for advanced e-commerce features, PAYARC gives you all the tools you need to optimize and grow your business.

Finally, if you’re in a higher-risk industry, you can’t go wrong with PaymentCloud. You’ll get tons of popular business software integrations and impressive security.

You can see how my top e-commerce processors stack up against each other in the table below.
Best Feature Best For Monthly fee on cheapest plan Transaction fees on cheapest plan
Leaders Merchant Services Room to negotiate an ideal pricing plan Hybrid businesses that take both in-person and online payments $9.00 ~2% + 0¢
PAYARC Custom plans and technology-driven e-commerce features Businesses that want a tailored approach to processing and impressive features N/A 2.49% + 30¢ (in-person)
ProMerchant Affordable pricing with essential e-commerce features Small businesses and startups $7.95 3% + 10¢ (credit)
Stax Advanced analytic tools Merchants looking for advanced tools and analytics $99.00 0% + 10¢ (in-person)
Flagship Merchant Services Month-to-month contracts with no cancellation fee First-time merchants $7.95 1.58% + 19¢ (in person)
PaymentCloud Support for mid- to high- risk businesses Merchants in industries considered higher risk $14.00 Around 2.1% + 15¢


How can I set up credit card payments on my website?

The answer to this can go two different ways. Most payment processors offer shopping cart integrations with a variety of website builders. These integrations make it simple to accept payments on your e-commerce website. If you didn’t build your website using a website builder, however, some payment processors like PAYARC offer custom APIs to help you accept payments on any site.

What is the best payment processor for e-commerce?

The ideal payment processor will vary from merchant to merchant. It all depends on your transaction volume, which features you need, and what kind of business you run. In general, though, Stax offers the best range of features and integrations for e-commerce.

What is the safest online payment system?

Every payment processor featured on this list offers highly secure e-commerce software, so it’s difficult to say for certain which is the most secure. Leaders Merchant Services offers Authorize.net which has end-to-end encryption, discounted SSL certificates for customers, and advanced fraud detection and prevention tools.

Is PayPal or Stripe better for e-commerce?

Both PayPal and Stripe offer a comparable service as they’re both e-commerce focused interchange-plus payment processors. However, neither are ideal for taking more than one-off payments due to the high per-transaction rates. It’s difficult to say which payment processor is the definitive best for e-commerce as that depends on your business model. To find a good option for you, check out our list of the best credit card processors in 2022.

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