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10 Best Payment Processing Software For Ecommerce In 2023

The Best Payment Processing Software List

Here’s a shortlist of the best payment processing software:

  1. Chargebee

    Best subscription solution for high-growth ecommerce companies

  2. Freshbooks

    Best payment processing with incremental/upfront/partial payment options

  3. Square

    Best payment processing app for small business

  4. Stripe

    Best for online retail businesses

  5. Helcim

    Best payment processing software for recurring billing

  6. Venmo for Business

    Best for startups & freelancers

  7. FTNI

    Best payment processing software for financial institutions

  8. KIS Payments

    Best for loyalty programs

  9. Fiserv

    Best payment processing platform for Asia-Pacific enterprises

  10. Elavon

    Best payment processing software for restaurants

The best payment processing software helps you sleep at night, knowing that your transactions are handled appropriately.

Whether you are an online business, startup, or an established business wanting to move online, the software on this list will improve your financial operations. How? Well, your customers can use a range of payment methods, including credit card payments and prorated invoicing. Creating this convenience brings more business, and the payment processing solution helps you manage all those transactions.

Additionally, it helps you set up recurring billing, protect against fraud, and safeguard customer payment information. The downside? You pay processing fees and monthly fees (depending on your usage), which can eat into your profits.

If you have general questions about this topic, skip to the FAQ section. Otherwise keep scrolling to get to the overviews, and you can always check how I picked the software on this list at the bottom of this article.

Overviews Of The 10 Best Payment Processing Software

Here’s a brief description of each payment processing software to showcase what each tool does best, including screenshots to highlight some of the features.

1

Chargebee

Best subscription solution for high-growth ecommerce companies

Chargebee is a subscription management platform that lets you automate subscription box billing and management, streamline order management, provide add-ons and gift subscriptions, and derive insights with detailed analytics.

Ecommerce managers can empower freedom of choice through customer self-serve portals. You can offer personalized options like customizable shipping and billing frequency for subscribe-and-save as well as box and membership subscriptions. You can easily add to your product line, and increase customer loyalty and lifetime value by intelligently bundling subscriptions with add-ons, accepting localized payments, offering promotions, gift subscriptions, resend/refund options, and more.

Chargebee integrates with tools for ERP, sales, finance, ecommerce, reporting analytics, marketing, collaboration, and customer support and success.

Chargebee costs from $249/month for 10 users and offers a free plan for up to 3 users. Chargebee also offers a free trial.

This is an aggregated rating for this tool including ratings from Crozdesk users and ratings from other sites.
4.6 528

Free 14-day trial

From $249/month

2

Freshbooks

Best payment processing with incremental/upfront/partial payment options

FreshBooks is an online payment processing system that helps businesses simplify invoicing customers, tracking payments, and managing expenses. It integrates with other popular tools, such as QuickBooks and Xero, to make it easy to sync data across multiple platforms. It offers a range of customizable invoice templates that make it easy to create professional-looking invoices and allows users to set up recurring invoices so that customers can be automatically billed on a regular basis. FreshBooks helps businesses manage expenses by allowing them to quickly enter bills and attach digital copies of supporting documents like receipts and invoices. This makes it easier to keep track of spending and ensure that everything is accounted for come tax time.

FreshBooks has built-in reminders that let users know when an invoice is past due, or a customer hasn’t paid yet. It provides insights into customer behavior, so users can better understand their spending habits. FreshBooks allows users to accept payments through their invoices via major credit cards or PayPal accounts. This makes it much easier for customers to pay quickly without waiting for a check in the mail or setting up additional bank transfers. The platform also offers automatic deposits so that any payments processed through their invoices are deposited directly into bank accounts.

FreshBooks includes detailed reporting tools that make it easier for business owners to manage their finances. Various reports are available for tracking revenue by customer or product and reports on expenses, taxes, and sales trends. The comprehensive reports help businesses stay organized by providing detailed insights into their finances to easily track how much money they're making or losing in any given period. FreshBooks also offers numerous security measures to protect users’ data and funds. All sensitive information is encrypted using industry-standard encryption technology, ensuring that all transactions are safe and secure.

FreshBooks costs from $15/month and offers a 30-day free trial.

30-day free trial

From $15/month

3

Square

Best payment processing app for small business

Square features a simple credit card reader that lets you accept payment from all major credit cards (Visa, Mastercard, Discover, etc.), and also from mobile payments like Apple Pay and Google Pay. You can store credit cards to charge repeat customers via recurring billing. You can also create custom invoices from your POS on your mobile or laptop and email them directly to your customers. Square has a virtual terminal feature that lets you bill customers remotely or by entering their details over the phone.

Square uses machine learning to conduct fraud detection, protection, and monitoring. Square has level 1 PCI data security standards that encrypt customer information that’s submitted to Square servers securely. It complies with the Payment Card Industry Data Security Standard (PCI DSS) so individual validation of compliance is not required. Square works out of the box with QuickBooks, WordPress, Squarespace, and similar apps.

For card-present payments, the fee is 2.6% + $0.10 per transaction. For card-not-present payments (where you have to manually key the details) the fee is 3.5% + $0.15.

This is an aggregated rating for this tool including ratings from Crozdesk users and ratings from other sites.
4.3 31

Freemium plan available

From $35/month

4

Stripe

Best for online retail businesses

Stripe enables your website to accept global payments from a variety of payment options, making it a good pick for online businesses. It enables payment solutions for online retailers, in-person retailers, and subscription-based businesses with recurring payment modules. The setup is simple and without complicated options. You simply connect your bank details, and it is good to go.

The platform is focused on optimizations with machine learning models training on billions of data points to improve conversions and improve security with revenue recovery and fraud detection. Stripe integrates with MailChimp, WordPress, Chargebee, BigCommerce, and other similar apps. Stripe has an extensive knowledge base and 24×7 email and chat support.

Pricing varies from country to country but is usually within 2% to 3% of the transaction.

This is an aggregated rating for this tool including ratings from Crozdesk users and ratings from other sites.
4.3 246

Contact Sales for more info

From 2.9% + 0.30 per transaction

5

Helcim

Best payment processing software for recurring billing

Helcim helps you accept credit cards easily from your device. With the Helcim virtual terminal, you can convert your computer, mobile, or tablet into a credit card processor. It lets you accept all major credit cards like Visa and Mastercard. It also enables the authorization of payments in seconds, with all the credit card information securely stored in its vault.

There is a feature for recurring payments where you can bill repeat customers with customized recurring payment plans. You can also directly sync the information with Quickbooks online. You can request payments via email or SMS and also send automated reminders. Helcim integrates with apps like Quickbooks, Magento, and WooCommerce.

For in-person payments, the pricing is 1.92% of the transaction amount + $0.08. For manually keyed transactions and online transactions, the rates are 2.44% + $0.25.

This is an aggregated rating for this tool including ratings from Crozdesk users and ratings from other sites.
4.4 13

Free account available

From 2.44% + $0.25 (average)

6

Venmo for Business

Best for startups & freelancers

Venmo is free payment processing software. You can accept or pay payments in the form of a credit card, debit card, or bank account. Venmo offers syncing with your phone contact or Facebook account, making it easier to find your contacts, request payment, or pay them. You can search people by their name, Venmo username, phone number, or email address.

The user experience is geared towards the average freelancer and is free of enterprise-level complexities. As an added security measure, each account comes with a unique QR code that lets you verify if you are paying the right person. A uniquely fun feature is adding GIFs or emojis with your payment description (you know you ain’t down with Gen Z until you pop up a few emojis!). The app is available on both Android and iOS and integrates with PayPal and Quickbooks.

Venmo does not charge any transaction fees for sending and accepting payments or for standard transfer to your bank account.

Contact Sales for info

From 1.9% + $0.10 per transaction

7

FTNI

Best payment processing software for financial institutions

FTNI helps streamline and automate accounts receivable operations. It lets you accept one-time and recurring payments from credit and debit card payments. FTNI’s ETran platform lets you deliver the flexibility to use your existing bank, merchant processor, and back-office relations to manage payment acceptance. FTNI can send customized invoices and securely accept checks, credit, and debit cards via the ETran mobile app.

FTNI does not list any integrations on its site. Customer support is available via email and chat. There’s also a knowledge base with step-by-step guides.

FTNI provides customized pricing upon request.

Demo available

Available upon request

8

KIS Payments

Best for loyalty programs

KIS payments enable business owners to accept any type of card securely and quickly. Its virtual terminal feature can convert your mobile device, desktop, or tablet into a credit card processing device. KIS payments also provide features for recurring billing so you can bill repeat customers with customized schedules. It also lets you launch a variety of loyalty programs to build relationships with customers.

KIS payments integrates with Elavon, Fiserv, and People’s Trust. It also partners with Ecwid to help you create online stores. Support is via phone, email, and live chat. There are also tutorial videos and guides to smarten you up on the workings of the app.

KIS Payments offers customized pricing upon request.

Free quote available

Available upon request

9

Fiserv

Best payment processing platform for Asia-Pacific enterprises

Fiserv offers automated payments processing across all payment types and about 60 clearing schemes, including high value, low value, SWIFT, BAHTNET, RENTAS, and G3. It offers a single payment platform for domestic and regional clearings, including Singapore, Malaysia, Indonesia, and Thailand.

Their real-time payment architecture allows you to add clearings and refine workflows according to your developed payment strategy. The app is compatible across all devices, be it mobile, tablet, or desktop. Fiserv does not list any integrations on its site. Support is via phone, email, and a ticketing system.

Fiserv offers customized pricing upon request.

Demo available

Available upon request

10

Elavon

Best payment processing software for restaurants

Elavon offers a secure merchant card processing service that is powered by PCI DSS compliance. Elavon lets you accept payment by credit card, debit card, and bank checks. Evalon also lets you take payments from Apple Pay, Samsung Pay, and Google Pay. It promises same-day transfer of funds to your account.

Evalon’s product Poynt provides a smart terminal solution for restaurants, helping them process counter-pay and pay-at-the-table transactions.In terms of security, Elavon has EMV authentication, encryption, and tokenization of data, thus keeping it safe from fraudsters.Elavon has a multilingual support team that is available via chat 24/7. There is also a knowledge base that lists step-by-step guides.

Elavon offers customized pricing upon request.

Contact Sales for info

Available upon request

The 10 Best Payment Processing Software Comparison Chart

Here are all the tools we just covered in a convenient table so you can compare them side by side.

Tool Free Option Price
1
Chargebee

Best subscription solution for high-growth ecommerce companies

Free 14-day trial

From $249/month Visit Website
2
Freshbooks

Best payment processing with incremental/upfront/partial payment options

30-day free trial

From $15/month Visit Website
3
Square

Best payment processing app for small business

Freemium plan available

From $35/month Visit Website
4
Stripe

Best for online retail businesses

Contact Sales for more info

From 2.9% + 0.30 per transaction Visit Website
5
Helcim

Best payment processing software for recurring billing

Free account available

From 2.44% + $0.25 (average) Visit Website
6
Venmo for Business

Best for startups & freelancers

Contact Sales for info

From 1.9% + $0.10 per transaction Visit Website
7
FTNI

Best payment processing software for financial institutions

Demo available

Available upon request Visit Website
8
KIS Payments

Best for loyalty programs

Free quote available

Available upon request Visit Website
9
Fiserv

Best payment processing platform for Asia-Pacific enterprises

Demo available

Available upon request Visit Website
10
Elavon

Best payment processing software for restaurants

Contact Sales for info

Available upon request Visit Website

Need expert help selecting the right Payments Facilitating Software?

We’ve joined up with Crozdesk.com to give all our readers (yes, you!) access to Crozdesk’s software advisors. Just use the form below to share your needs, and they will contact you at no cost or commitment. You will then be matched and connected to a shortlist of vendors that best fit your company, and you can access exclusive software discounts!

Other Payment Processing Software Options

Here are a few more that didn’t make the top list but are still worth looking into if you need more options.

  1. Unity Payments - Best payment processor for fundraising
  2. Recurly - Best payment processing system for subscription-based businesses
  3. Plooto - Best payment processing app for cash monitoring
  4. Podium - Best text-to-pay software
  5. Tipalti - Best payment processing software for PO matching
  6. ChargeBee - Best payment processor for B2B SaaS startups
  7. HoneyBook - Best invoice customization app 
  8. PayIt - Best payment processing software for public sector
  9. FiveStars - Best payment processing tool for local businesses 
  10. eBiz Charge - Best email-integrated payment processing software
  11. Amazon Pay - Best payment gateway for large enterprises
  12. GoCardless - Best payment processor with pre-built payment flows
  13. PayPal Enterprise - Best payment processor for checkout optimization
  14. PlateIQ - Best accounts payable life cycle management software
  15. Synder - Best payment software for small to mid-sized ecommerce businesses
  16. First data - Best merchant service for invoice and payment automation
  17. Worldpay - Best payment processing software for fraud detection

Pro tip: You might also consider pairing your payment processing software with ecommerce fraud prevention software to block phony purchases or chargebacks.

How I Picked The Best Payment Processing Software

Let me explain how this whole process went down. First, I evaluated and compared the most popular payment processing tools on the market, both for their reviews and user interface. Then I took that initial list and weighed factors that make software a good option for payment processing, such as the ones that follow. 

User Interface (UI)

Is it clean and attractive? Is the menu simple and without any clutter? This tool is going to handle most of your revenue. Therefore, it needs to be easy on the eye and show information clearly. You don't want to mess up with numbers!

Usability

Almost every industry needs a payment processing app to process payments. To cater to this wide range of user base, payment processing software should be extremely easy to use and be without any complicated set-ups. A key factor is the level of support provided with the app, in the form of direct help and via knowledge bases.

Integrations

Is it easy to connect with other tools? The best payment processing apps work out of the box with landing pages, accounting software, and other apps. Therefore, I'll look at pre-built integrations, third-party services, and custom integrations using an API.

Pricing

Is pricing clear, transparent, and flexible? These tools usually have costs divided into percentages plus a fixed fee. I will highlight that information for you or if you need to contact Sales.

Not Looking for Payment Processing Software?

Try these articles if you aren’t looking for payment processing software but still need some help with other ecommerce tools:

Payment Processing Software FAQs

To make this list of best payment processing software for ecommerce businesses even more comprehensive, I wanted to cover some of the most frequently asked questions on the topic.

What's Next?

These were my top selections for the best payment processing gateway software. But while we are on this topic, how about you learn what buy-now-pay-later platforms are? I think it's relevant because there is a case to be made that not using them can actually damage your business.

Also, if you liked this list, I would really appreciate it if you can share it on your social media channels. Who knows who you might be helping with this useful information!

Want to stay ahead with all things related to ecommerce management? Subscribe to The Ecomm Manager Newsletter and stay ahead with the latest insights from top thinkers in the Ecommerce industry.

By Francois Marchand

I’m Francois Marchand, content strategist and editor. I've worked in marketing, journalism, and communications for 20 years. I've been in charge of creating and managing content at Postmedia, Vancouver Film School, and Unbounce. I love helping business leaders, content creators, and marketers of all stripes grow their skillsets and knowledge base to stay ahead of the competition.

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