How to Accept HSA/FSA Payments—What the Best Businesses Know

Millions of Americans have health savings accounts (HSAs) and flexible spending accounts (FSAs), and they’re eager to spend those pre-tax dollars on products and services that help them feel better, live longer, and stay healthy. If you own a health business and you don’t know how to accept HSA payments, you’re not just missing out—you’re leaving serious money on the table.

The good news? Accepting HSA and FSA cards is far easier than most founders think, and it can help your business grow its customer base, boost sales, and ultimately lead to happier customers. Here’s everything you need to know about how to accept HSA payments, how eligibility works, and why it matters for your business’s growth.

What are HSA and FSA? Quick Overview

Before diving into how to accept HSA and FSA payments, let’s get clear on the basics. Here’s the difference between HSA vs. FSA accounts:

• Health savings accounts: HSAs are tax-advantaged accounts available to people with high-deductible health plans. Funds roll over year to year and can even be invested, making HSAs a long-term tool for healthcare savings.
• Flexible spending accounts: FSAs are employer-sponsored accounts that let employees set aside pre-tax dollars for eligible health expenses. Unlike HSAs, funds are “use-it-or-lose-it” within the plan year.

The government created both accounts to cover HSA- and FSA-eligible expenses, such as:

• Doctor visits
• Prescription medications
• Copays
• Dental care
• Vision care
• Medical equipment

But coverage isn’t limited to clinical care — with proper documentation, many health products and services (like supplements, fitness programs, or sleep tools) can also qualify if they meet certain criteria.

Why Your Business Should Consider Accepting HSA/FSA Payments

For business owners in the health and fitness industries, the benefits of accepting HSA and FSA dollars extend well beyond simply offering another payment option, says Rami Sneineh, a licensed insurance producer and vice president of Insurance Navy Brokers.

And for businesses outside of traditional healthcare (like supplements or fitness programs), Truemed provides the compliance pathway through letters of medical necessity, so you can access this market too (more on that in a moment).

According to Sneineh, here are the other upsides to consider:

• Bigger customer base: “It may assist in acquiring a new customer base: the people who use their tax-saving medical-related expenses funds to cover their costs,” says Sneineh. In other words, when you accept HSA/FSA cards, you unlock access to millions of consumers who already have money earmarked for health expenses and are actively searching for ways to spend it.
• Boost sales and loyalty: Pre-tax dollars feel different to customers: This is money they’ve already set aside, and many have a deadline to use it. That urgency drives higher conversion rates and larger cart sizes. “This not only results in more revenue, but it can also result in increased customer satisfaction since more people will choose to go to a business that offers the convenience of using FSA/HSA cards,” says Sneineh. Put simply, you’re not just making a sale—you’re building long-term loyalty.
• Competitive advantage: Many health-conscious consumers specifically search for stores that accept FSA cards or HSA payments. If a competitor offers that option and you don’t, you risk losing those sales. On the flip side, being among the first in your category to integrate HSA/FSA acceptance gives you a powerful edge.

How HSA/FSA Cards Work—and If Your Business Qualifies

So, what is an FSA or HSA card, and how do they work?

Think of them as debit cards tied to a tax-advantaged account, says Sneineh. Customers swipe, tap, or enter the card number online just like with any other card. The primary difference lies in how they can spend those dollars.

“These [cards] are targeted at qualified medical expenses,” he explains. “Compared to standard debit cards, FSA/HSA cards have more restricted usage and should be utilized on permitted healthcare expenses, such as prescription medicine, medical equipment, and services.”

Because of this restriction, HSA/FSA cards are designed to work automatically at businesses classified under healthcare-related merchant category codes (MCCs)—think pharmacies, clinics, or medical equipment suppliers. If your business doesn’t fall into one of those categories, card transactions may decline by default.

But that doesn’t mean other products and services (like supplements, fitness equipment, or gym memberships) can’t qualify. Under IRS Section 213(d), products or services that diagnose, cure, mitigate, treat, or prevent a medical condition can be qualified, HSA/FSA-eligible medical expenses. Where a product or service has both a medical and non-medical use, it can qualify if it's backed by a letter of medical necessity (LMN) from a licensed provider.

An LMN is a note from a healthcare provider that documents why a specific product or service is medically necessary for someone’s health condition. With an LMN, everything from strength training programs for metabolic health to sleep products for insomnia may become HSA/FSA eligible.

Truemed makes this process seamless for both businesses and customers. To partner with Truemed, first sign up as a merchant. After that, the Truemed team will help determine the eligibility of your products, and if eligible, begin the implementation process so your customers can shop your products with Truemed.

When customers shop your business via Truemed, they'll be prompted to complete a health survey, and if they're eligible, based on their survey, a licensed provider will issue them an LMN. This LMN then makes your product eligible for HSA/FSA spending.

From there, the experience is simple for your customers: They purchase your product with their HSA/FSA card (no reimbursements necessary) or with their everyday credit or debit card, then submit their receipt and LMN to their HSA/FSA provider for reimbursement.

When customers shop through that link, they’ll complete a health questionnaire, and if appropriate, a licensed provider will issue them an LMN. This LMN then makes your product HSA/FSA-eligible.

From there, the experience is simple for your customers: They purchase your product with their everyday credit or debit card, then submit their receipt and LMN to their HSA/FSA provider for reimbursement.

This expands HSA/FSA eligibility far beyond traditional medical providers, opening the door for supplement brands, fitness platforms, digital health products, and other businesses to unlock pre-tax dollars as a growth channel. In fact, customers typically save ~30%* when using HSA/FSA funds.

How to Accept HSA/FSA Payments: Step-by-Step

The process of accepting HSA/FSA cards may seem intimidating at first, but it’s more straightforward than most founders realize. Here’s what to do.

Step 1: Confirm Eligibility of Your Products or Services

“In the case of businesses, it is necessary to ascertain the eligibility of goods or services to be bought using FSA/HSA cards in order to remain in compliance with the IRS stipulations,” says Sneineh.

Some products (like prescription medications or medical devices) are automatically eligible under IRS Section 213(d). But many health products outside of traditional categories can also qualify if a medical professional considers them necessary. Truemed bridges this gap by facilitating LMNs when appropriate, helping businesses make more of their products compliant without the headache of navigating IRS rules alone.

Examples of what FSAs and HSAs can be used for include:

• Doctor visits
• Mental health therapy
• Prescription drugs
• Medical devices
• Weight loss or fitness programs prescribed for a chronic condition
• Supplements*
• Fitness equipment*
• Gym memberships*
• Sleep products*

*Eligibility for these items requires an LMN. For a full overview of potentially eligible products and services, see our ultimate list of HSA/FSA-eligible items.

To stay compliant, businesses should also proactively communicate by clearly labeling HSA/FSA-eligible products on their site, training customer support, and providing documentation as needed.

Finally, “it is important to keep pace with the IRS practices because rules often vary from year to year,” says Sneineh.

Step 2: Set Up Payment Processing for HSA/FSA Cards

“Businesses have to incorporate the right payment system that acknowledges and accepts these transactions,” Sneineh says. This often means using a payment processor that deals in healthcare payments.

Fortunately, most modern payment processors (like Stripe, Square, and Payrix) can accept HSA/FSA cards as long as your MCC aligns with healthcare categories, or you work with Truemed to provide LMNs that make your products eligible.

Step 3: Implement Seamless Online Checkout

The key to a smooth experience is making HSA/FSA use feel just like a normal purchase. That means integrating the option clearly at checkout and removing as much friction as possible.

Here’s how to set it up:

• Make eligibility visible: Add “HSA/FSA eligible” tags or badges on product pages so customers know before they hit checkout.
• Offer clear payment instructions: If you’re a Truemed merchant, direct customers to your Truemed link where they can receive an LMN (if appropriate).
• Keep checkout simple: Customers then pay with their everyday credit or debit card and submit their receipt and LMN to get reimbursed by their HSA/FSA provider.
• Provide support. Add a short FAQ or help section at checkout answering common questions like “How do I use my HSA/FSA with this purchase?”

Step 4: Clearly Communicate Your Acceptance of HSA/FSA Payments

Don’t keep this benefit a secret. Once you’ve set up HSA/FSA acceptance, Sneineh recommends making sure customers are aware:

• Add “HSA/FSA-eligible” callouts on product pages so customers see it before they buy. Highlight it alongside price and benefits to reduce friction at checkout.
• Include the option at checkout, both in-store and online, so customers immediately recognize they can use pre-tax dollars.
• Promote it in your marketing and email campaigns. A simple “now accepting HSA/FSA” announcement can drive new and repeat purchases from customers actively looking for ways to spend FSA and HSA funds.
• Train your customer support team to answer common questions. Being able to guide customers through the process builds trust and keeps them coming back.

Common Challenges and Solutions for Accepting HSA/FSA Payments

Even with the right setup, a few hurdles can come up. The key is knowing how to handle them smoothly. Here are some common challenges, and what to do if they happen:

• Declined cards: Transactions may fail due to ineligible products, insufficient funds, or technical errors. “At times, a trivial problem such as an invalid product category or technical fault can lead to failure of a transaction,” says Sneineh. “In the event that the product is qualified, check that the customer has a sufficient amount in his or her card to purchase the product.” If it’s eligibility-related, though, be transparent and offer alternatives. In the event of a system issue, train staff to troubleshoot or guide customers on reimbursement.
• Changing IRS rules: Sneineh recommends that business owners stay updated on industry-specific changes. Eligibility rules shift over time, so monitor IRS publications and follow processor updates.
• Customer confusion: Many customers don’t know which products and services qualify. Clear signage, “HSA/FSA-eligible” tags online, and well-trained staff can reduce friction and turn confusion into confidence at checkout.

How Customers Use HSA/FSA Cards

From the customer perspective, using an HSA or FSA card feels almost identical to paying with a debit or credit card. But there are a few important differences that can impact their experience and your sales. Here’s what to keep in mind:

• They swipe, tap, or enter online: Customers use their HSA/FSA card at checkout just like any other card, says Sneineh, and they expect the same speed and ease.
• Ineligible items may decline: If the purchase doesn’t qualify, the card won’t process. Customers then either switch to another payment method or pay upfront and submit receipts for reimbursement.
• FSA deadlines create urgency: Because FSA dollars often expire at the end of the year, customers are motivated to use them before they disappear. Businesses that highlight eligibility capture this demand.
• Clarity drives trust: The more you make eligibility obvious, the less confusion and frustration your customers will feel, says Sneineh.

The bottom line: The easier and clearer you make the process, the more likely customers are to use their pre-tax funds with you and keep coming back.

Examples: Stores that Successfully Accept FSA/HSA Payments

Businesses across the health and fitness industries are already tapping into the power of pre-tax spending and reaping the rewards. Here are some common examples of stores that accept FSA and HSA cards:

• Pharmacies and clinics: National chains like CVS and Walgreens have long accepted FSA/HSA cards for prescriptions, over-the-counter medications, and health supplies. Independent clinics and practices also benefit by making it easy for patients to use their pre-tax funds on visits and procedures.
• Digital health platforms: Telemedicine services, online therapy apps, and virtual care platforms increasingly accept HSA/FSA cards. This not only broadens access to care but also lowers financial friction for patients who prefer digital-first solutions.
• Health brands: Forward-thinking supplement companies, fitness programs, and sleep product brands are finding ways to qualify under IRS rules, especially when paired with medical evaluations that document necessity. For example, a medically supported weight-loss program or fitness membership may qualify as HSA-eligible when prescribed for a chronic condition.

Through Truemed, even more brands in categories like supplements, sleep, and fitness are able to qualify with LMNs, turning what used to be out-of-pocket expenses into HSA/FSA-eligible purchases.