PayJunction Review 2021: Features, Pricing, Alternatives

Learn all about PayJunction, and explore a few alternative options to help choose the best PSP for your business.
Brian O'ConnorJan 30, 2020

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If your small business wants to accept payments, be they in-store or through your online store, you’ll need to select the best payment service provider (or a PSP) for your company’s needs.

This PayJunction review covers everything you need to know about PSPs and dives into the details of PayJunction’s major features and pricing to help you make your best decision.

It’s easy for almost any business to accept cash, but credit cards offer more convenience and flexibility for customers. The best small-business strategies accept a mix of both cash and credit; and if your business does any selling online, being able to accept credit cards online is absolutely crucial.

This is where PSPs come into play: companies like PayJunction and others enable stores and e-commerce merchants to accept credit cards and other digital transactions (such as PayPal, Apple Pay, Google Pay or ACH payments) either in-person with physical terminals or online through a secure payment gateway.

These payment processors route information from your customers’ bank and onto yours in order to get you paid, regardless of whether your customer swipes a card or manually inputs their credit card information. These services encrypt sensitive information and make sure that the details end up in the right place — all to help make sure your business gets paid rapidly every time someone flashes plastic at your store (whether that store is brick-and-mortar or digital).

In short, PSPs like PayJunction take care of the messy business behind the scenes that make it possible for businesses to accept everything aside from cash (although they can help you keep track of that, too).


PayJunction’s toolkit includes a payment gateway, a point-of-sale (POS) terminal that can handle card transactions whether or not the card is present, and a few other features that help automate and streamline essential processes.

Smart terminal: PayJunction’s cloud-based POS terminal can accept EMV, NFC, swipe cards and Apple Pay payments. This plug-and-play terminal digitally stores your customers’ signatures and all transaction histories, which you can then easily search if the need arises down the line; then, your customers will have the option of a printed or emailed receipt. PayJunction also claims that its Smart Terminal processes payments almost four times faster than the average POS terminal, which better ensures a frictionless checkout process for both you and your customers.

ACH payments: In addition to accepting all types of credit and debit cards, PayJunction can securely accept ACH payments at low transaction fees (0.75%, to be exact). If your customer pays via ACH check, you’ll collect their signature digitally and send them an emailed receipt.

E-commerce merchant services: If you run an e-commerce business, PayJunction can act as both your payment gateway and your merchant account so you can securely accept payments online — just customize and embed its hosted checkout button on your business website and let PayJunction handle the PCI-compliant payment processing. PayJunction integrates with over 80 popular shopping carts, like 3D Cart and Magento.

Mobile app: With PayJunction’s free mobile app, iOS users can accept keyed-in credit card payments right from their phone or tablet.

Additional payment processing features: PayJunction also offers a few time-saving features that streamline and automate the payment process, all while keeping both your customers’ and your business’ security top of mind. For instance, the Smart Terminal can securely store credit, debit and ACH information so you can easily search and refund purchases recharge repeat customers with one click, or to set up recurring billing. Plus, PayJunction can remotely capture signatures for card-not-present transactions to protect you against chargebacks.

Analytics: Use PayJunction’s native analytics tools to view a range of financial reports, like trends and comparisons over time and transactions by card type. And since all your data is securely stored in the cloud, you can easily search and export reports and transaction histories to keep for your records.

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PayJunction uses interchange-plus pricing with a markup of 0.75% for all credit card transactions. If you’re already working with a payment processor and you’re looking to switch to PayJunction, PayJunction will provide you with volume-based pricing based on two months of billing statements.

Also, PayJunction has no long-term contracts, so you don’t need to worry about an early cancellation fee. It also won’t charge you a monthly, annual or PCI compliance fee, or a fee for your payment gateway. The only exception is businesses that process under $10,000, which will need to pay a $35 monthly fee.


PayJunction is a truly comprehensive payment processor that should be especially appealing to small-business owners who want to digitize the checkout process and their records. But with so many payment processors available to small-business owners, it makes sense to consider how PayJunction stacks up against the competition.


You’re likely aware of Square, a tech-forward platform that got its start as one of the first end-to-end payment service providers for small-business owners. The merchant services company has since expanded to include even more tools and services for SMBs, like Square Capital, Square Payroll and Square Appointments, but let's focus on Square POS and Square Payments, the platform’s marquee products.

Square Payments is a scalable and customizable payment processing solution that enables your business to accept all forms of tender however you need to, whether that’s in person, over the phone, via mobile or on your website. You can either choose to integrate Square Payments with third-party POS hardware, like Lavu and Vend, or choose among Square’s own range of POS hardware: Square Register ($799), its most powerful countertop solution; Square Stand ($199), which enables you to accept chip and contactless payments through your tablet;  Square Terminal ($399), a compact countertop register; or Square Readers ($10-$49), which plug into your phone or tablet so you can accept credit cards on the go.

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on Square's website

Beyond processing payments, Square’s software can help you manage a range of back-end processes, too, like inventory tracking, employee management, analytics, payroll, marketing and CRM tools, though these tools may cost you extra. Square does offer users free basic software with the Square POS app, which is compatible with both Apple and Android devices. Square also provides specialized POS systems for certain types of businesses, like retailers, restaurants, salons and professional services.

Square runs on a pay-as-you-go model, and its per-transaction fees vary depending on which POS tool you’re using and which kind of payment you’re accepting. You can take a look at Square fees to determine exactly how much you’ll be paying for every transaction processed.


Clover is a highly customizable, all-in-one POS solution that can accept all types of payment, including EMV cards, NFC cards, swipe cards, checks and cash. Clover really shines in its in-person payment processing hardware, so e-commerce businesses may do better with another payment processor designed to integrate with online stores.

But if you want to accept physical payments at your brick-and-mortar location, over the phone or on the go, you’ll have the option of Clover’s four POS solutions:

  • Clover Station (starts at $1,199): A fully outfitted countertop register, complete with a cash drawer and receipt printer.

  • Clover Mini ($599): A smaller version of Clover Station.

  • Clover Flex ($449): A handheld, cloud-based POS system that accepts all types of credit cards.

  • Clover Go ($69): A cloud-based mobile card reader that lets you accept credit payments on your smart device.

On top of its hardware range, Clover also provides a virtual terminal so you can accept payments online.

Clover offers two service plans — Register Lite ($14 per month) or Register ($29 per month) — that provide users with various payment processing and business management tools, including offline payment processing, employee shift planning, financial reports and access to the Clover App Market, which collects hundreds of third-party apps that integrate with your Clover system. Clover provides tailored solutions for specific industries, too, including retailers, service and repair businesses, restaurants and quick service businesses.

Clover also offers flat-rate transaction fees, but those fees vary depending on which software plan you choose. With Register Lite, you’ll pay 2.7% plus 10 cents per transaction for in-person transactions, or 3.5% plus 10 cents for keyed-in transactions. If you sign up for the Register plan, you’ll pay 2.3% plus 10 cents for in-person transactions and 3.5% plus 10 cents for keyed-in transactions.

A version of this article was first published on Fundera, a subsidiary of NerdWallet