The Best Payment Processing Software List
Here’s a shortlist of the best payment processing software:
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Free 14-day trial
|From $249/month||Visit Website|
30-day free trial
|From $15/month||Visit Website|
Freemium plan available
|From $35/month||Visit Website|
Contact Sales for more info
|From 2.9% + 0.30 per transaction||Visit Website|
Free account available
|From 2.44% + $0.25 (average)||Visit Website|
Contact Sales for info
|From 1.9% + $0.10 per transaction||Visit Website|
|Available upon request||Visit Website|
Free quote available
|Available upon request||Visit Website|
|Available upon request||Visit Website|
Contact Sales for info
|Available upon request||Visit Website|
Need expert help selecting the right Payments Facilitating Software?
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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.
- Unity Payments - Best payment processor for fundraising
- Recurly - Best payment processing system for subscription-based businesses
- Plooto - Best payment processing app for cash monitoring
- Podium - Best text-to-pay software
- Tipalti - Best payment processing software for PO matching
- ChargeBee - Best payment processor for B2B SaaS startups
- HoneyBook - Best invoice customization app
- PayIt - Best payment processing software for public sector
- FiveStars - Best payment processing tool for local businesses
- eBiz Charge - Best email-integrated payment processing software
- Amazon Pay - Best payment gateway for large enterprises
- GoCardless - Best payment processor with pre-built payment flows
- PayPal Enterprise - Best payment processor for checkout optimization
- PlateIQ - Best accounts payable life cycle management software
- Synder - Best payment software for small to mid-sized ecommerce businesses
- First data - Best merchant service for invoice and payment automation
- 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!
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.
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.
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 is payment processing?
What is payment processing software?
What are the key features for payment processing software?
What is a payment gateway?
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!
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