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  5. 6 BEST Healthcare Credit Card Processing Companies in 2023

6 BEST Healthcare Credit Card Processing Companies in 2023

Emma Ayres Emma AyresFinance Specialist May 18, 2023
May 18, 2023
Finding the right credit card processor is challenging for any business, but if you’re in the healthcare sector, there’s even more to consider.

That’s because not every processor offers HIPAA-compliant software or can integrate with software medical offices commonly use. And even those that do may not offer pricing models well-suited to your business. Just because one type of merchant account works for a physiotherapy clinic doesn’t mean it’ll work for a pharmacy.

That’s not to say you’re out on your own. I’ve researched dozens of credit card processing companies, and I’ve found some fantastic options that come with HIPAA-compliant software, excellent rates, and even free hardware. Stax is my top choice as its vast suite of HIPAA-compliant payment tools come included in its monthly fee. Plus, it offers tons of built-in security features to keep your data safe.

Let’s take a look at the best healthcare payment processing for medical offices available today.

Short on Time? These Are the Best Healthcare Credit Card Processors For Medical Offices in 2023

  1. Stax – HIPAA-compliant payment and business management software included in the monthly fee.
  2. Payment Depot – Budget-friendly payment processing with an impressive security record.
  3. Leaders Merchant Services – Negotiable pricing model backed by a money-saving guarantee.

See 3 More Great Options | Comparison Table | FAQ

What We Look For in the Best Healthcare Credit Card Processing For Medical Offices

There’s no one-size-fits-all approach to healthcare payment processing, but there are features that every medical office needs from its credit card processor.

  • HIPAA-compliant software. Software that’s used to access or store patient information needs to be HIPAA-compliant. Every payment processor on this list has its own software or can integrate with HIPAA-compliant software tools, making it easier to manage your administrative tasks.
  • E-commerce integrations. Whether you take appointment bookings online or allow patients to order and pay for their medication on your website, you’ll need e-commerce integrations to handle those transactions.
  • Chargeback and fraud protection. Chargebacks and so-called “friendly fraud” can present a significant threat to healthcare businesses, particularly when insurance companies don’t cover as many costs as the patient expects. Good healthcare merchant accounts come with built-in protection against fraudulent chargebacks and aid in disputing them if they arise.
  • Invoicing and payment plans. Depending on your practice, you may have patients that need to spread out the full cost of their bill or need extra time to pay your invoice. A good payment processor should give you a variety of payment plans so that your patients can pay for their treatment in whatever way suits them best.

A Note on HIPAA Compliance

Credit card processing itself is not considered a HIPAA-covered activity because you’re not storing any health-related information in your merchant account. If you’re only using a payment processor for this purpose, then it doesn’t need to have a BAA or be HIPAA-compliant.

However, any software you use – whether that’s built into your merchant account or offered as a third-party integration – needs to be HIPAA-compliant if it has access to personal health information (PHI). This includes the tools you use to manage invoices, bookings, health records, or any other aspect of your practice.

Stax summary
Stax gives you all the HIPAA-compliant software you need to manage your healthcare practice
Offering both 0% markup on interchange fees and a full suite of HIPAA-compliant software for a single monthly fee, Stax is one of the best healthcare payment processors for high-volume medical offices. If you already use various software tools to manage your healthcare business, Stax can save you a significant amount on software fees alone. Overall, healthcare businesses can save up to 40% on their payment processing with Stax.

Every Stax plan gets you access to Stax Pay, which comes with financial analytics and reporting, a virtual terminal, and even an online customer review management dashboard. The Pro plan unlocks Stax’s powerful invoicing software, which you can use to set up branded invoices with embedded payment links.

Most importantly, Stax’s built-in security ensures your patients’ PHI remains secure. Stax is a PCI Level 1 credit card processor, which is the highest level of PCI compliance available. This means it needs to complete third-party security audits every year, have its network scanned quarterly, and employ an internal compliance team. It also uses end-to-end encryption and tokenization to keep your data secure.

Features and Benefits

  • Accept FSA/HSA. Stax merchant accounts can accept payments directly from a patient’s FSA or HSA account, making it even easier for your patients to pay you on time.
  • Payment plans. You can set up payment plans on Stax’s Ultimate plan, which is ideal for healthcare practices that regularly charge for expensive procedures that clients may not be able to pay for in one go. You can also store payment methods for patients with recurring billing.
  • Fraud protection. Stax uses address verification (AVS) to detect potentially fraudulent transactions. If AVS can’t completely verify a customer’s identity, Stax will put a hold on their account until you receive additional verification.
  • 24/7 support. Stax offers 24/7 phone support and a comprehensive knowledge base. If you run a busy healthcare practice and can only contact support outside of business hours, it’s good to know someone’s always available at Stax to help you out.
Read more about this processor’s software suite in our expert Stax review.

HIPAA compliant?
Fraud and chargeback support
  • Customer account holds
  • Chargeback support phone line
  • Transaction filters, transaction holds, AVS (
Other security features
  • PCI Level 1 compliant
  • PCI compliance support for merchants
  • Tokenization, end-to-end encryption
Transaction fees on cheapest plan 0% + 10¢ (in-person)
Monthly fee on cheapest plan $99.00

Payment Depot summary
Payment Depot is surprisingly humble about its top-of-the-line payment security
If you process a high volume of transactions each month but are working to a strict budget, Payment Depot is a great choice for your medical office. With Payment Depot, you’ll pay an affordable monthly fee in exchange for 0% markups and a low flat transaction fee of 8¢. It’s one of the most budget-friendly credit card processors for healthcare, particularly given its exceptional security features.

Not only is it PCI Level 1 compliant, but Payment Depot is GDPR compliant too. This is completely voluntary because Payment Depot is an American company that doesn’t serve merchants in Europe. GDPR is a fairly complex set of regulations, but a key highlight is that Payment Depot can’t store data for any longer than necessary. This limits the risk of harm to you and your patients in the unlikely event of a data breach.

All data is protected by end-to-end encryption, which turns your data into a string of unidentifiable numbers and letters during transmission between servers. Card information is also tokenized, meaning that it’s replaced with a unique set of characters during transmission so that sensitive data never leaves your local network or Payment Depot’s servers unprotected.

Features and Benefits

  • 24/7 risk monitoring. Payment Depot’s risk monitoring team constantly monitors changes in fraud methods and bank policy, which allows Payment Depot to build security solutions before a problem arises.
  • Easily dispute chargebacks. You can dispute chargebacks directly from your Payment Depot dashboard. Not only is this convenient, but it’ll save you from having to switch between multiple tabs while you search for the billing and transaction information you need.
  • Great security record. Payment Depot has never suffered a data breach. This is a good indication that it works hard to keep its systems secure and up to date, so you can be sure your data is safe.
  • integration. The popular payment gateway is included with your Payment Depot plan  and comes with even more security features for e-commerce. It uses pre-built and customizable transaction filters to identify and hold potentially fraudulent transactions.
Read more about payment security in our in-depth Payment Depot review.

HIPAA compliant?
Fraud and chargeback support
  • Built-in chargeback dispute system
  • Transaction filters, transaction holds, AVS (
Other security features
  • PCI Level 1 compliant
  • GDPR compliant
  • Tokenization, end-to-end encryption
  • 24/7 risk monitoring team
Transaction fees on cheapest plan 0% + 10¢ (in-person)
Monthly fee on cheapest plan $79.00

3. Leaders Merchant Services: Negotiate a Good Deal

Leaders Merchant Services summary
Leaders Merchant Services offers competitive pricing to help you grow your healthcare business
Leaders Merchant Services (LMS) promises to meet or beat your current processing rates. It’s so confident that it can at least meet your current rates, it’ll give you a $200 AMEX gift card if it can’t. So, if you’ve been with your current credit card processor for at least two months, get in touch with an LMS sales agent – there’s a good chance that this credit card processor can offer you lower rates.

On top of some of the lowest per-transaction rates I’ve seen in an interchange-plus pricing model, you can also get free POS hardware if you’re willing to sign a long-term contract. You may also be able to negotiate multiple free terminals depending on your contract length and business needs. This goes to show the lengths LMS is prepared to go to provide the best solution possible for your specific healthcare business.

LMS itself isn’t HIPAA-compliant, however, and neither is most of the software it integrates with. That said, LMS is a certified Clover reseller, and Clover’s POS software is HIPAA-compliant. It even comes with additional management tools like invoicing, staff scheduling, and CRM software.

Features and Benefits

  • Merchant cash advances. LMS offers merchant cash advances to all its customers. If you’re unable to qualify for traditional financing, you’ll still be able to secure funding for your business through LMS.
  • 96% approval rate. If you’ve struggled to find a credit card processor for your healthcare business in the past, give LMS a try. In some cases, you’ll know whether you’ve been approved on the same day, and you’ll be able to start taking payments in a few days.
  • Add-on services. You can also negotiate additional services like loyalty programs and subscription payments, both of which can be extremely helpful for medical offices and specialized services.
  • 24/7 phone support. This is ideal for healthcare practices that take after-hours emergencies. No matter what issue you’re having, you can count on LMS support for help.
Read more about negotiating your rates in our Leaders Merchant Services review.

HIPAA compliant? No, but integrates with Clover software that is
Fraud and chargeback support Transaction filters, transaction holds, AVS (
Other security features
  • PCI-compliant
  • Tokenization, end-to-end encryption
  • PCI compliance support for merchants
Transaction fees on cheapest plan ~2% + 0¢
Monthly fee on cheapest plan $9.00

Flagship Merchant Services summary
Flagship Merchant Services is one of the few payment processors that offer Clover hardware for free
If you’re on a budget but still need modern POS hardware, then you should consider Flagship Merchant Services. As with LMS, you’ll be able to negotiate the best pricing model, rates, and software for your business – and you’re covered by the same meet-or-beat guarantee. This, however, is where the similarities end.

That’s because Flagship offers free Clover Mini devices – provided you meet certain requirements that aren’t disclosed on the website. Clover devices aren’t cheap to purchase outright, so getting one for free can save you a lot of money if you need modern, smart POS devices for your healthcare practice. Just be aware that you’ll have to pay an extra cost to use Clover’s HIPAA-compliant software.

Features and Benefits

  • Same-day funding. While this comes at an extra cost, it’s ideal for meical offices that need a consistent cash flow to stay afloat.
  • Business financing. Flagship offers cash advances of up to $150,000 for all merchant accounts, which are paid back as a commission on future sales.
  • Quick setup. Unlike other credit card processors, Flagship’s onboarding process is pretty fast. Once you’ve been accepted, you can start processing payments on the next business day.
  • iAccess business portal. This software suite is HIPAA-compliant and allows you to see sales summaries, generate financial reports, and even analyze how well your business is doing against the competition.
Read our Flagship Merchant Services review to see more great features.

HIPAA compliant? No, but integrates with software that is
Fraud and chargeback support Transaction filters, transaction holds, AVS (
Other security features
  • PCI, GDPR, & CCPA compliant
  • Tokenization, end-to-end encryption
  • Regular merchant account security scans
Transaction fees on cheapest plan 1.58% + 19¢ (in person)
Monthly fee on cheapest plan $7.95

Luminous Payments summary
Luminous Payments focuses on in-person payments for small, local businesses
Luminous Payments is ideal for community-focused small healthcare clinics. While you’ll get some software included, like HIPAA-compliant shopping carts for your website and the fantastic NMI payment gateway, Luminous is best for brick-and-mortar medical offices.

Once you’ve been approved for a merchant account (which usually happens on the same day you apply), Luminous Payments will send you a free B250 Bluetooth card reader to get you started. If you’ve already got POS hardware, you can get these reprogrammed for free, providing your devices meet modern security standards.

You’ll also be able to save money on your credit card processing by using Luminous Payments’ Cash Discount Program. This effectively lets you pass your per-transaction fees onto customers that pay by card, so you only have to budget for the small monthly fee.

Features and Benefits

  • Same-day funding. Luminous Payments offers next-day funding as standard, but if you need to access your money sooner, you can pay a small extra monthly fee for same-day funding.
  • Guaranteed Savings Program. If you’re already processing card payments with another business, Luminous Payments guarantees it will either meet those rates or offer you a cheaper deal. If it can’t, you’ll get $1,000 upon signing.
  • Certified Clover reseller. Luminous Payments assists in selecting and setting up the ideal Clover devices for your business. Clover’s POS hardware, known for its excellence, is available in the market and can be paired with HIPAA-compliant business and payment management software for an extra monthly fee.
  • Custom pricing. In addition to the Cash Discount pricing option, Luminous Payments offers interchange-plus, tiered, and flat rate pricing models. You can also negotiate a custom pricing model to suit your healthcare clinic’s needs.
See how Luminous Payments can help your community clinic in our expert review.

HIPAA compliant? No, but integrates with Clover software that is
Fraud and chargeback support Transaction filters, transaction holds, AVS (NMI)
Other security features
  • PCI-compliant
  • PCI compliance assistance for merchants
  • Tokenization, end-to-end encryption
  • NMI gateway is GDPR compliant and offers two-factor authentication
Transaction fees on cheapest plan 1.59% + 5¢ (qualified)
Monthly fee on cheapest plan $10.00

6. Big Savings for High-Volume Clinics

Payment Depot summary offers a variety of subscription-style pricing models
High-volume healthcare practices stand to save a lot of money with subscription-style pricing models.’s High Volume plan is one of the best on the market. As with Stax, you’ll pay a flat monthly fee, no interchange markup, and a small transaction fee, which can save you a lot of money if you’re processing hundreds of thousands of dollars each year. also offers free Clover Minis on its most expensive High Volume plan, and if you’re happy to commit to a one-year contract, you can get a free Pax A920 terminal on all other plans. High Volume plans also come with a dedicated account manager to support you with any questions or issues. The only snag is the highly monthly cost, which stands at $15.00.

With that being said, the higher transaction fees on its more affordable plans aren’t enticing for smaller businesses, either. If you run a smaller, high-volume medical office, you’ll likely save more money with Stax.

Features and Benefits

  • High approval rate. If you’ve got a low credit score, give a try. It claims to have the highest approval rate in the US, and you can get set up within 24 hours.
  • 24/7 PCI support. You can contact a PCI compliance expert over the phone or email to get support with filling out your PCI documentation. This is ideal if you’re new to payment processing and you need an extra helping hand.
  • Data breach insurance. If suffers a data breach and you suffer any financial losses as a result, you’re covered for up to $100,000.
  • Free training. Once you’ve been approved for a merchant account, offers free training to help you learn how to use your POS hardware and the iAccess business portal.
Read our review to see how you could save money.

HIPAA compliant? No, but integrates with Clover software that is
Fraud and chargeback support Transaction filters, transaction holds, AVS (
Other security features
  • PCI-compliant
  • PCI compliance assistance for merchants
  • Tokenization, end-to-end encryption
  • Data breach insurance
Transaction fees on cheapest plan 0% + 30¢ (Starter)
Monthly fee on cheapest plan $15.00

Which Is the Best Healthcare Credit Card Processing Company for Your Clinic?

It’s not always easy to find payment processors that offer affordable rates, HIPAA-compliant software, and great customer service. While there’s no one-size-fits-all solution, these are my top recommendations that will suit most healthcare businesses.

Overall, my top pick is Stax. If you process over $5,000/month, Stax can help you save up to 40% on your processing fees. Plus, every Stax merchant account comes with HIPAA-compliant business and payment management tools.

Payment Depot offers similar savings, and its monthly plans are designed to be more accessible for small businesses. It has a fantastic security record and it’s one of the few credit card processors that is voluntarily compliant with GDPR, so you can be confident that Payment Depot will keep your data safe.

Finally, if subscription-style pricing doesn’t work for your medical office, I recommend Leaders Merchant Services. With some of the cheapest per-transaction fees in the industry and a fantastic meet-or-beat guarantee, you’ll be able to negotiate the best possible rates for your healthcare business.

Here’s how the best healthcare credit card processing providers compare.
Best Feature Best For Monthly fee on cheapest plan Transaction fees on cheapest plan
Stax HIPAA-compliant business and payment management software Modern healthcare businesses that need a powerful software suite $99.00 $99.00
Payment Depot Budget-friendly subscription pricing Security-conscious healthcare businesses that want built-in data protection $79.00 $79.00
Leaders Merchant Services Pricing models that are open to negotiation Healthcare businesses looking to secure cheaper processing rates $9.00 $9.00
Flagship Merchant Services Free Clover Mini devices for qualifying merchant accounts Healthcare businesses that need modern POS hardware for their clinic $7.95 $7.95
Luminous Payments Cash Discount pricing model that helps you to save on fees In-person healthcare clinics looking to reduce their overhead costs $10.00 $10.00 Subscription-style pricing for high-volume merchants High-volume healthcare clinics looking to save money $15.00 $15.00


Which payment platforms are HIPAA-compliant?

Both Stax and Payment Depot are HIPAA-compliant. If you need modern business software for your healthcare business, Stax is a good choice. However, you can still use a non-HIPAA-compliant payment processor to accept credit cards within your clinic as this is classed as an exempt activity. If you need to use payments software like e-commerce platforms, shopping carts, or scheduling software, then you’ll need to check that it offers a BAA for healthcare businesses.

What payment platforms are HIPAA-compliant?

There are a lot of HIPAA-compliant payment platforms on the market. For high-volume healthcare businesses, I recommend Stax. This payment processor offers a payment gateway, CRM, analytics software, and marketing integrations for one flat monthly fee. If subscription-style pricing doesn’t work for your business, take a look at Leaders Merchant Services, which has some of the lowest rates on the market and plenty of modern payment tools to support your business.

Why is PayPal not HIPAA-compliant?

PayPal isn’t HIPAA-compliant as it doesn’t offer a BAA (Business Associate Agreement) to healthcare providers. On top of that, PayPal collects user data and sells it to advertisers, so there’s no guarantee that it would protect PHI. If you need a HIPAA-compliant payment solution that offers great software, no contracts, and competitive pricing for small businesses, it’s worth checking out Payment Depot.

What is the most common violation of HIPAA?

The most common HIPAA violation is the failure to secure and encrypt Public Health Information (PHI). When it comes to payment processing, you can prevent this by using a processor that provides HIPAA-compliant software. You should also train staff that collect payments in data security. This means ensuring that payments taken over the phone are done so in an area where PHI cannot be overheard and shredding documents containing PHI after use.

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