Paychex Credit Card Processing Review 2023

Credit and Debit Card Processing

Paychex offers the ability to accept all major credit and debit cards, and provides an option for next-day funding. If you accept international transactions, Dynamic Currency Conversion is available to provide receipts in your customer’s home currency.


You’ll be able to accept payments by phone using your PC, using a smartphone or tablet, or in person with a traditional POS system or countertop terminal.

Phone Payments

Paychex offers the VirtualMerchant solution for turning your existing computer into a secure payment machine. With an internet-based portal there’s no software to install and you’ll be able to enter card details directly into a secure form. Virtual terminals are a great choice for those that take payments by phone or for businesses that don’t need special processing equipment. You can optionally add accessories like card readers and receipt printers.

Mobile Payments

You can use the VirtualMerchant Mobile app for taking on-the-go payments with a smartphone or tablet. VirtualMerchant is available for Apple and Android devices, can collect customers’ signatures through the touchscreen of your phone or tablet, and allows you to email receipts to your customers. For added security and faster card entry, you can attach a card reader instead of keying in card details.

ACH and Check Processing

In addition to payment by credit card, Paychex allows for ACH transactions and check processing. The company offers electronic check conversion services and direct ACH, eliminating the need to make physical deposits at the bank and potentially enabling faster funding.

Zero-Cost Credit Card Processing

Paychex’s zero-cost credit card processing option lets you automatically pass the costs of processing to customers when they check out. It’s essentially an automated surcharge. Surcharging is only allowed on credit cards, and only in states that don’t have laws prohibiting the practice.

Read more about zero cost card processing.

Intelligent Rate

Similar to zero-cost, Paychex offers an “Intelligent Rate” solution for government and educational organizations. Intelligent Rate works to customize convenience fees or service fees for each customer, proportional to the cost of the card they use. For example, a customer using a debit card may pay less in service fees than a customer using a rewards credit card.

Intelligent Rate works by calculating the cost of the card in real-time, as the consumer enters payment information. However, it’s important to note that the costs of cards aren’t finalized until the transaction is settled. The Intelligent Rate calculation is an educated guess as to the cost of the card, but actual costs may end up different than estimated.

Intelligent Rate is only available for the following merchant category codes:

  • 9311 – Tax
  • 9222 – Fines
  • 9211 – Court Costs
  • 9399 – Miscellaneous Government Services
  • 8220 – College Tuition
  • 8244 – Business
  • 8249 – Trade Schools
  • 8211 – Elementary and Secondary Schools

Read more about merchant category codes.

Additional Services

In addition to payment acceptance services, Paychex offers tools to benefit other aspects of your business, such as QuickBooks integration for accounting purposes or marketing and design services to help promote traffic to your business.

Dental and Medical Practice Integration

Paychex integrates with some dental and medical practice management software, including TotalDental, PIMSY, CounSol, Umbie DentalCare, and more.

Integration with practice management software eliminates the need for manual entry and time-consuming reconciliation between multiple systems. This option is available when using Paychex payment processing through its partner BluePay.

QuickBooks Integration

Paychex offers a plugin to integrate with QuickBooks accounting software if you use Bluepay for your processing. The plugin enables batch processing, payments from invoices, automatic payments, and tokenization for security. However, you will not be able to enter Level 3 data, so if you take a lot of corporate or government cards, this solution might not be ideal.

The plugin is compatible with QuickBooks Pro, Premier, and Enterprise in version 2012 or later, as well as QuickBooks Online and Point of Sale.

Marketing and Design

Paychex offers several marketing and design services, including a user-friendly website builder for non-programmers to create a functional, attractive website. The company handles hosting and offers a drag-and-drop interface that includes thousands of templates to choose from. You can add an ecommerce module if you intend to sell products or services through your site as well.

The ecommerce option integrates with credit card payment acceptance, and lets you easily view and manage orders, send order confirmations, and more.

If you’re just getting started, Paychex’s design services include a logo design option, letting you work with the company’s designers to create a custom logo. If you’re further along, Paychex also offers account managers that can help with SEO, keyword research, and other essentials for modern websites.

Equipment for Payment Processing

For full-featured point of sale systems, Paychex offers the NCR Silver iPad POS system. As noted in this NCR Silver review, the system offers plenty of features, including inventory management, employee tracking, store and forward modes for when your internet connection is down, and more. Paychex doesn’t specify costs for equipment.

Paychex also references smaller EMV chip-capable countertop terminals, but doesn’t provide details on brands or models available.

Paychex Credit Card Processing Costs

Paychex doesn’t publish costs for credit card processing, simply stating that they offer clear pricing with no hidden termination fees, allowing you to cancel at any time.

As mentioned previously, there is also a “zero cost” option, which is actually an option to surcharge customers at the time of sale to cover fees. Zero cost processing cannot be used on debit cards and is only available in states where surcharging is not prohibited by law.

Clear and Simple Program

For businesses that don’t process many payments and are looking for ocassional processing, Paychex offers a “Clear and Simple” program with the following published charges:

Monthly fee: $10
Swiped rate: 2.75%
Swiped per-transaction fee: $0.29
Keyed rate: 3.5%
Keyed per-transaction fee: $0.29

Curious how Paychex pricing compares to other processors? View comparisons for your specific business using a free processing quote comparison tool.

Paychex Reviews

Paychex is better known for its payroll and HR services than for payment processing. The company launched its credit card processing options in 2014, but reviews available online focus primarily on the payroll side of things. The general complaints claim that the company has poor customer service.

Paychex has a profile at the Better Business Bureau website, where it has been accredited since 2010 and maintains an A+ rating.

Paychex reviews

However, the company has also had 200 complaints lodged with the BBB in the past 3 years, as well as 17 negative reviews. Again, reviews are most commonly about payroll and HR services, not payment processing. Complaints allege Paychex makes frequent mistakes including failing to file taxes. Many reviewers complain that the types of mistakes Paychex makes result in hassles for the business.

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