Best Online Payment Processing Tools for Small Businesses

Posted on February 29, 2024 | Updated on February 29, 2024

Small businesses need an online presence to survive in today’s market. E-commerce is a great way to capitalize on these channels, but running an effective web store can be tough. On top of several other considerations, you’ll need the best online payment processing services to do it.

Accepting payment online isn’t as straightforward as it is in person. You’ll need a third party to manage these transactions, so choosing the right one for your needs is a big decision. 

The Best Online Payment Processing Services

While every business has unique needs, a few payment processors stand above the rest. Here’s a glimpse at five of the best online payment processing tools for small businesses today.


Square made a name for itself through in-person credit card transactions, but it supports online payments, too. The company processes over $50 billion a quarter, making it one of the most popular options, and it’s easy to see why.

The service has no monthly charges, operating solely on a 2.9% plus 30¢ transaction fee. There are also no activation, cancellation or industry compliance fees. Square also offers automation, analytics and invoicing features at no extra cost.

The biggest downside to Square is that it doesn’t offer around-the-clock support. The company also doesn’t work with “high-risk” businesses — those likely to have high return volumes or face higher fraud risks.

Shopify Payments

Shopify is one of the best e-commerce platforms, and its transaction tool is one of the best online payment processing systems. The service comes as part of Shopify’s broader e-commerce solution, making it a natural choice for businesses already using the platform.

Like Square, Shopify charges a 2.9% plus 30¢ fee for online transactions. Companies with an Advanced Shopify e-commerce plan can get lower fees, though. The service also accepts a wide range of payment types, is relatively easy to set up and is highly customizable.

Unfortunately, you need a Shopify e-commerce plan to use Shopify Payments, introducing at least a $29 monthly rate. There are additional fees for using third-party gateways and a $15 chargeback fee.


Stripe is a solid alternative for businesses that don’t already use Shopify. The service is similar to Square but focuses on online channels. It also focuses on customization, making it easy to integrate into custom checkout processes.

Stripe’s pricing follows the industry standard of 2.9% plus 30¢ per transaction. It also has no monthly fees or setup costs and offers 24/7 support.

Personalization is perhaps Stripe’s biggest advantage, but it comes at a cost. Businesses need developer experience to make the most of its customizable features. It also doesn’t work with high-risk businesses.


PayPal is another one of the best online payment processing solutions and a familiar site for many businesses. Over three-fourths of the top 1,000 retailers use it in some capacity. It’s most popular as a gateway, but you can use it as a processor, too.

Because PayPal is so widely used among both consumers and businesses, it offers an easy, familiar checkout experience for customers. It also supports many flexible payment methods, including cryptocurrency.

In terms of drawbacks, PayPal is on the expensive end. There are no monthly fees, but it charges between 1 and 4% plus 49¢ per transaction. There’s also a $20 chargeback fee, and support isn’t available 24/7.


Helcim is a less familiar name for many but is still a solid alternative. The company offers multiple merchant services, but you can use it solely for online payment processing if that’s all you need.

Helcim supports many payment options, from credit cards to QR codes. It also has many convenient features like a mobile app, inventory management tools and sales analytics. Its base price is 0.5% plus 25¢, which is cheaper than many others, and prices are even lower for businesses with more sales.

Despite those low costs and the lack of monthly fees, Helcim does charge a $15 chargeback fee. It also doesn’t offer around-the-clock support or work with high-risk merchants.

What to Look for in an Online Payment Processing Tool

Any of these five processors is a good option, but the best online payment processing service depends on the specific business. Here are some things to consider to find the right one for your needs.


The most obvious factor to weigh is how much the service costs. Of these five, Helcim is the cheapest, especially for high-volume e-commerce businesses. However, that doesn’t necessarily mean it’s the best for everyone.

Shopify may initially seem more expensive, but its rates are competitive if you already pay for its e-commerce platform. Considering Shopify accounts for 26% of the entire e-commerce market, many businesses fall under that category.

It’s also worth considering fees for things like setup, contract termination, refunds and chargebacks. Stores that expect a lot of situations like this should opt for a service without these fees, even if its rate is higher. Any operational expenses incurred from disruption if a platform doesn’t work with the company’s current tech suite are also worth noting.

Compatibility with Your Business Model

Businesses should also consider how a payment processor fits within their business model. A blockchain-centric tech startup should probably accept cryptocurrency payments, so PayPal may be the way to go. Companies with unique approaches to customer service or highly tailored websites may prefer Stripe for its customizability.

E-commerce stores should consider their sales volumes, too. Business models reliant on large amounts of small sales should look for processors with volume discounts. Those relying on fewer but larger sales may save more through one with lower per-transaction rates but a monthly fee.

Compatibility extends to the tools your business uses, too. The average company uses more than 200 SaaS apps, and if a payment processor doesn’t integrate with any of these, it’ll cause workflow bottlenecks and other complications.

Ease of Use

Similarly, the best online payment processing tools are also easy to use. If a system is cheap but too complicated to operate efficiently, it may not produce significant real-world savings.

What defines “easy” depends on a business’s current workforce. A tech-savvy team could use a highly personalized but code-heavy platform like Stripe relatively easily. Others may struggle with it, making simpler platforms like Square a better choice.

It’s important to consider ease of use from a customer viewpoint, too. Emphasizing the customer experience is key to growing a business, and the checkout process is a big opportunity to do so. Look for an option that integrates well into your e-commerce site and supports your customers’ preferred payment options,


Ongoing support is another crucial factor to consider. Regardless of a processing platform’s ease of use, issues can still arise. Having access to around-the-clock customer support makes dealing with these problems much easier.

Businesses with more tech experience may not need as much support as others. The same goes for companies that only operate within normal business hours. However, 24/7 help is never a bad thing, especially with a more complicated processing system.

Find the Best Online Payment Processing Tool for Your Business

As e-commerce keeps growing, so do online payment processors. This choice is great news in light of businesses’ diverse needs, but it also means finding the best one can be more challenging.

These five solutions are some of the best online payment processing services available today. Start with this list, write out your needs and find the tool that’s right for you.

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About The Author

Eleanor Hecks is the Editor-in-Chief of Designerly Magazine, an online publication dedicated to providing in-depth content from the design and marketing industries. When she's not designing or writing code, you can find her exploring the outdoors with her husband and dog in their RV, burning calories at a local Zumba class, or curled up with a good book with her cats Gem and Cali.

You can find more of Eleanor's work at

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