How Do I Set Up HSA Payments on My Website?

A health savings account (HSA) and a flexible spending account (FSA) allow qualified customers to use pre-tax dollars to cover qualified medical expenses outlined by the IRS. These purchases include FSA/HSA-eligible items and services that treat and prevent physical ailments and mental illness, with eligibility ultimately determined by plan rules.

Enrolled account-holders with a high-deductible health plan (HDHP) can open an HSA. FSAs are a workplace benefit (typically employer-managed) with plan-specific restrictions and deadlines.

HSA/FSA cards run on major card networks such as Visa and Mastercard. So, HSA/FSA card payments can be accepted in-person or online—if the issuer supports card-not-present payments and the merchant configuration code (MCC) accepts HSA/FSA cards. Services like Truemed allow merchants who are not able to get an MCC that accepts HSA/FSA to still unlock HSA/FSA spending.

Not all qualifying customers use an HSA/FSA card at checkout. Depending on their plan, some customers pay with a standard card and later submit an itemized receipt for reimbursement from their FSA or HSA account.

There are three main merchant eligibility paths that allow businesses to accept HSA payments.

• A healthcare-related MCC. Approved healthcare merchants, like pharmacies with the associated MCCs, can accept HSA-eligible purchases at checkout.
• SIG-IS registration and the 90% rule. The Special Interest Group for IIAS Standards (SIG-IS) assists merchants in complying with card network regulations to accept HSA/FSA card payments. Merchants whose sales are primarily eligible health expenses (90% or more) may be designated as healthcare merchants and may have simplified transaction processing. This path requires merchant attestation but still streamlines the virtual checkout process for customers.
• Eligibility-focused checkout integration. This path makes sense for merchants who don’t have an eligible MCC or who don't meet the 90% threshold. Merchants with a mixed catalog of HSA-eligible and non-eligible items need a smart checkout integration that can determine eligibility based on the item’s inventory SKU. The system can identify items at checkout that are generally FSA/HSA-eligible but may require customers to acquire a letter of medical necessity (LMN) for items that are not automatically eligible, and generate itemized receipts to substantiate purchases.

An IIAS (Inventory Information Approval System) is a point-of-sale technology that ensures only eligible expenses are purchased with an HSA/FSA card. Retailers with an approved healthcare MCC don’t require an IIAS, but retailers that also sell non-eligible items may be required to use an IIAS to accept HSA/FSA cards. In turn, this will impact the processors you can use.

It may seem complicated to set up HSA payments online, but the general process can be straightforward.

First, confirm that your current MCC and business category align with your payment processor. Approved healthcare merchants with the associated MCCs can enable HSA-eligible products to be pre-approved at checkout. Misaligned MCCs with payment processors are a common cause of HSA/FSA card declines. For retailers using the 90% rule path with SIG-IS for accepting HSA cards, complete the self-attestation steps and keep required registrations up to date. Confirm with your processor if HSA/FSA cards must be explicitly enabled on your account, as some processors require configuration or approval.

Also, plan for card-not-present constraints and give eligible customers different payment options. Some HSA/FSA cards will work online only if the issuer allows it. In these instances, the eligible customer may have to pay with a personal card and submit a reimbursement request later through their plan, so ensure your system offers itemized receipts. If your system allows, consider adding an ACH payment option (an electronic transfer of funds) for HSA accounts that provide routing or account details.

To give eligible customers a smooth checkout experience, offer two payment paths: pay with an HSA/FSA card or pay now and use receipts for reimbursement. Don’t make coverage guarantees or promise outcomes that only the HSA/FSA plan administrator can confirm—use contingent language.

The checkout system should handle mixed carts or flag HSA-eligible and non-eligible items for the customer. When possible, it should separate eligible and non-eligible items or clearly explain to customers how mixed carts may impact payment authorization. The system also must generate substantiation-friendly itemized receipts. This means that receipts have clear product or service descriptions, per-item costs, purchase date, and merchant details. Ensure receipts and refund confirmations are easy to access for customers.

If HSA/FSA cards are declining at checkout, there are a few strategies that can help determine why.

Test HSA/FSA cards from multiple issuers, including Visa or Mastercard-branded cards, to determine if the declines are tied to a specific card issuer. Check other common issues: MCC mismatch with business category and processor, the checkout system not handling mixed carts, issuer security blocks on card-not-present capabilities, different HSA/FSA plan restrictions, and whether the checkout system is missing an eligibility path setup.

As you determine the cause of HSA/FSA card declines, set an alternative customer support path customers can try—without guaranteeing eligibility. Options include splitting mixed carts, using an alternate payment method, or requesting reimbursement through their plan after using a non-HSA/FSA credit or debit card. If, after you’ve tested different cards and checked common causes for declines, you are still unsure why HSA/FSA card purchases decline, then you should contact your processor to confirm the account is properly configured for HSA/FSA cards.

To stay compliant, language is important. Retailers should always use contingent language, like “may be eligible,” and specify that any claims may be considered product- and condition-specific. Note that an independent licensed practitioner will determine whether an LMN is appropriate, and that plan administrators make final reimbursement decisions.

Avoid prohibited phrasing, like “doctor,” “doctor’s note,” and “quick survey” or anything that implies a time limit to the process. Also, avoid words like “guaranteed,” “approved,” or “wellness.”

Merchants can work with Truemed* to enable qualified customers to use HSA/FSA funds for potentially eligible products and services related to a diagnosed medical condition. This helps businesses twofold: with payment processing as well as new customer acquisition. For online checkout, merchants can add a “Pay with HSA/FSA” option, powered by Truemed, for qualified customers. Here, when applicable, customers complete a clinical intake form that will be reviewed by an independent licensed practitioner to determine whether an LMN is appropriate. If they qualify, the customer may be eligible to use HSA/FSA funds, depending on medical need and their plan rules. Truemed also processes pre-approved products without a health intake survey.

For qualified customers, both payment methods should be supported: using an HSA/FSA card at checkout when eligible or paying with a standard card and submitting itemized documentation for reimbursement. Because HSAs and FSAs use pre-tax money, customers using Truemed typically save an average of 30%.

*Truemed is for qualified customers. HSA/FSA tax savings vary. Learn more at truemed.com/disclosures.