10 Best Ecommerce Credit Card Processors For Your Store In 2021 (Merchant Accounts)

Written by Frank Hatchett

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Our goal at EcomElites is to help readers get the information they need, we partner with companies to help bring you that information. If a purchase or signup is made through our partners, we receive compensation for the referral. Learn More

Once you’ve started your E-commerce store, the next step is to choose a credible credit card processor for your store. The best ecommerce credit card processors offer more than just a safe and secure transaction.

Double check the fees laid out by each company and be sure the transaction charges levied on you, the business owner, are competitive.

A trustworthy credit card processor not only converts more visitors but also adds an element of authority to your brand. Utilizing well known and trusted vendors can be just as valuable to your brand as a great store aesthetic.

What is a Credit Card Processor?

To put it simply, an E-commerce credit card processor is an online payment system that allows the user to pay for their purchase securely.

There are many E-commerce credit card processors in the online marketplace however, not all of them are reliable. We’ve compiled a list featuring some of the best E-commerce credit card processors  to help you choose the right partner for your store.

These are the features you should be considering when searching for a payment partner.

PCI Compliance– The payment processing industry standard for data security (PCI DSS) is a set of security standards designed to safeguard the online payment process.

PCI is managed by PCI SSC, an independent council created by major credit card brands including MasterCard, Visa, Discover, American Express, and JCB. PCI covers nearly all major card issuers.

For an organization to be one of the top-rated E-commerce credit card processors, it must comply with PCI SSC guidelines. Remember, “SSL” has nothing to do with PCI DSS. An SSL certificate ensures that the website is loaded securely. It doesn't have much of an impact (if any) on PCI DSS compliance.


Buyer Protection– Another feature of major E-commerce credit card processors is complete buyer protection.  The processor itself helps the buyer quickly complete and manage online transactions. For example, PayPal, as a payment gateway, offers users special discounts, a user-friendly app, and easy integrations with other commonly used products.

Easy integration– Some of the best Ecommerce card processors allow the user to integrate their account in just 1-3 days. If you’ve entered all the correct details, the processor should be able to authenticate the information within 3 days at the max.

Fast payment processing– If your account is pre-integrated and your internet isn’t down an E-commerce payment processor should take just a few seconds to process and confirm payment.

Trustworthiness– Today, data privacy is a major topic of discussion and concern all for people around the globe. Integrity and transparency are crucial elements, especially if you are running an E-commerce store. If the E-commerce credit card processor you are using isn’t extremely trustworthy with an impeccable reputation, chances are visitors will never convert into customers.

Best Ecommerce Credit Card Processors In 2021

1: PayPal


Charge: 2.9% per transaction

PayPal is one of the most popular and best ecommerce credit card processors available today. PayPal offers a fully-secure transaction window while keeping its mechanism flexible.

They charge a fee of 2.9% per transaction and do not require any monthly subscription.  This flexible fee structure makes it perfect for small E-commerce stores, or online shops using the dropshipping model.

The PayPal UX is smooth, and the processing system is lightning fast, making for a great user experience. It’s an excellent choice for retailers with low monthly sales or those just getting started. PayPal offers basic POS (point-of-sale) features & simple integration.

Another point to make in the case for PayPal is the unfettered access to support you can rely on as a customer.

The company maintains a vast Knowledge Base, regularly updated forums, and ultra-responsive customer service, which you can reach via phone or email.  To set up a virtual terminal, you pay just $30 per month for “PayPal Payments Pro.”

The final verdict? This E-commerce credit card processor is easy to set up and incredibly flexible. If your store has good traffic and lots of transactions.

2: Stripe

stripe credit card processor

Charge: 2.9% plus $0.30 cents per transaction

Stripe is another one of our favorite E-commerce credit card processors for your online store. Stripe offers a fixed fee and charges 30 cents per transaction. PayPal doesn't support payment processing to North Korea, Bangladesh, and many other countries.

Restricted countries could vary based on where your business is domiciled. Stripe, on the other hand, does support payment processing for all those countries and many more.

The company’s free API allows you to create a custom checkout experience in your E-commerce store. Stripe is easy to work with and can be used to handle in-app purchases and marketplace transactions efficiently. Stripe makes it easy to make a payment with their custom gateway.

Stripe is a young but quickly growing company and is a great alternative gateway.

3: Square

Charge: 2.75% per transaction

Square is simply an awesome payment processing system. We believe it to be the best mobile credit card processor out there, thanks to its simplistic UX, low transaction cost, and quick integration system.

This E-commerce credit card processor works seamlessly with both the IOS as well as Android devices. It’s a good choice for small business as it doesn't charge a monthly fee.

Square offers several hardware solutions including Magstripe, contactless, and chip, terminals, stands, and registers, to help you accept payments anywhere you do business. Their customer support is stellar.

Square is a perfect processor for all types of E-commerce models, including online food stores, retail shops, and service providers. Square even offers powerful software for effortlessly managing employees and sales.

All these features together make it an ideal solution for all types of businesses. If you look at the complete package, Square is definitely a better option than PayPal.

4: Flagship Merchant Services


Charge: 2.30-2.50%

Flagship Merchant Services is a #1 rated merchant account provider for the last eight years. Flagship offers POS (point-of-sale) systems and smart terminals to give you the smoothest transactions no matter what your unique needs are.

Flagship is an E-commerce credit card processor with EMV/NFC terminals which enable payments through chip cards and other methods.

Flagship offers a low cost per transaction, and this credit card processor is entirely PCI compliant, ensuring the highest level of protection from fraud. Flagship provides all around solutions for most business types, including products for In-store, Mobile, Online, or MOTO. To make sure transactions are fast, they offer same days approvals.

The best part about Flagship is that they have a long-running reputation for trustworthiness among small and mid-sized businesses. They are always willing yo help there suppliers and clients succeed!

5: Amazon Pay

credit card processor

Charge: 2.90% per transaction

Amazon pay is one of the best credit card processor that seems to be the future of the industry. Since Amazon is such a well-known brand world over, it’s relatively easy for visitors to trust this credit card processor in a wide range of E-commerce stores.

It’s an excellent payment solution with no monthly, annual, or PCI fees. The downside is that it takes around 5 days to get access to the funds. This time frame is a bit longer as compared to other credit card processors, but you can expect a better conversion.

Amazon’s simplified checkout experience makes it easy for customers to pay using their Amazon account. No need to enter credit card data. After a few months working with them, it is possible to request they offer a more favourable reserve term.

Amazon pay is primarily available for U.S based businesses at the moment. The Amazon support system is robust, and you can use their knowledge base to easily setup Amazon Payment on your E-commerce store.

To get in touch with their sales team, you can submit a form on their website and can seek basic support over the phone, online chat, and via e-mail. This is one of the best ecommerce credit card processors to use in America.

6: Fattmerchant

best credit card processor- Fattmerchant

If you have just started your E-commerce store and want a good, introductory credit card processor, Fattmerchant is the option you are looking for.

Fattmerchant was designed for small businesses and stores with seasonal sales. They even offer a pause feature for the off-season. This company provides flat, subscription-based, and interchange-plus pricing.

If you have a pre-established E-commerce store with reasonable sales, we'd definitely recommend you to consider this option as well, they’re doing a lot right.

This E-commerce credit card processor offers tons of tools to help you efficiently manage and accept online payments. They support all the possible options for accepting payment. You can use POS hardware, web application, on-website, virtual terminal method, or even a card reader on your mobile phone to take payments.

Fattmerchant does not charge any early termination fees. This processor offers options compatible with most POS systems. When your store isn’t generating sales, the pause brings your costs down to just $25 per month from the regular $99. Fattmerchant offers excellent live support 24/7, in addition to its massive knowledge base.

7: Helcim

helcim ecommerce credit card processor

Helcim is an E-commerce credit card processor with a clean, transparent pricing model. They have different pricing scales for Non-profit organizations, in-person sales, and online sales.

  • In person sales: 0.25% plus 8 cents
  • Online sales: 0.45% plus 25 cents
  • Sales to non-profit organizations: 0.1% plus 10 cents

There are no early termination fees with Helcim; however, this may not be the best choice for a business generating fewer than 15,000 monthly transactions. You can expect serious discount offers when your shop reaches higher monthly sale volumes.

Helcim supports third-party integrations, including Shopify, Magento, and other popular E-commerce platforms. You can also export transactions to a .CSV file to populate other, non-supported apps. Helcim has excellent customer ratings and boasts an A+ with the BBB (Better Business Bureau).

Easy to follow “How-to” guides make it easy to get started and set up the processor in your web-shop. Helcim makes mobile payments, including Android pay and Apple Pay, secure and streamlined. If you have a multilingual store, you can enable multi-currency services using Helcim.

This means your customers can pay with their preferred currency.  The support is responsive and incredibly helpful. Combine that with all the other great features offered up by Helcim, and you’ve got a recipe for an excellent partner to new dropshipping stores.

8: Shopify

square credit card processor

Shopify is a complete E-commerce solution, everything from an E-commerce platform to a credit card processor is provided by Shopify.

Shopify is compatible with Oberlo and thus makes it easy to set up a dropshipping store in a matter of minutes. Shopify offers a POS for making your E-commerce business run smoother as it grows. They boast a variety of mobile payment options and is an ideal choice for those who don't want to invest in a lot in an E-commerce solution on its own.

The most affordable Shopify plan starts at $9 per month and a per transaction fee of 2.9% plus 30 cents. In addition to a pre-integrated POS, it supports plenty of third-party apps to help you provide a professional E-commerce experience to your audience while simplifying the way you do business at the same time.

You can use apps like printful and Oberlo to source products for your store without even needing to leave the Shopify platform.

Shopify generates a custom reports for all sales, which makes managing your shop a breeze. The Shopify app is compatible with all browsers, and the mobile app works flawlessly with both major types of devices (Android and iOS).

Shopify customer support is unparalleled. You can use their official email, request a live chat, get help via phone call, or use Twitter to get support 24/7.

9: Payline


Payline is an independent sales organization that pairs up perfectly with all sizes of business. Payline Data offers an easy to understand, affordable pricing plan. They have some great plans for low volume sellers too. Their two main payment plants are:

  1. Start: Provides support for countertop POS terminals and mobile POS devices. The “Start” plan costs 0.2% plus 10 cents per transaction and a $10 monthly fee.
  2. Connect: This plan is specially designed for E-commerce vendors. It’s an online payment gateway with premium security features and integrations.

Additionally, Payline offers a unique, discounted pricing structure for non-profit organizations. Payline is PCI compliant, and they do not charge any early termination fees. You can easily manage invoices through Payline, making it a good choice for high-risk merchants.

10: First Data

first data processor

First Data is one of the best credit card processors in the U.S. It’s an awesome choice for E-commerce stores with a high volume of sales. This credit card processor caters to merchants from over one hundred countries. If your E-commerce store has a nice volume of visitors, First Data is definitely worth a look.

First Data merchant services is one of the world's largest credit card processors. They have a well-trained support staff to help you with every E-commerce related issue you might come across.

While First Data is not the cheapest option, it does have a lot to offer in comparison to other processors. One of the things that make First Data stand out as one of the best credit card processors for retail is its negotiable pricing.

If a merchant has a large volume of transactions, they can often secure more favourable terms and more competitive pricing. If you’re targeting an audience in China, this is a great option, as it supports AliPay.

First Data offers clover processing equipment, perks for veterans, tools to help build loyalty programs for your customers, and a handful of other unique value-adds that you just don’t see in the competition.

11: Payment Depot

Payment Depot is a cost-effective whole sale credit card processor, which can be super lucrative for businesses that operate at specific volumes.

They have a variety of membership plans for businesses of all sizes. You can apply by filling out an online application. Payment Depot offers an Interchange-plus pricing , and their subscriptions range from $49-$199 per month.

They charge a per transaction fee of $0.15-$0.05 in addition to the interchange rate. You can purchase an annual subscription with a 90-day satisfaction guarantee which allows you to request a full refund if you decided to go with another processor.

What Payment System Is Best For You?

PayPal is a popular choice and is used by many E-commerce stores, but don’t get fooled into thinking it’s your only option. There are several really powerful providers out there that can make your business more productive with features and services that meet your unique needs.

Stripe is an excellent option if your audience-base is from some other country, Square is an option for small to mid-sized business.

If you are planning a long-term growth and looking to capitalize on easy conversions, Amazon Pay could be a better fit for you. Take the time to examine your needs and investigate options that will support you and your company’s goals.

You need to watch our for chargebacks when selling online. This article here will explain how they work.

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