Can a Shopify store accept HSA or FSA cards?

What does Shopify document about HSA and FSA cards?

Shopify documents a route on Shopify Payments: its help page for the United States says businesses in the United States that sell medical products might be eligible to accept HSA or FSA cards at checkout after a review. Among the review's conditions: the store owner makes the request, at least 90% of sales are medical products, and those products belong to one of the IRS approved categories. To verify eligibility, you must contact Shopify Support.

Vendor apps are a separate route: only approved Partners can build payments extensions on Shopify's Payments Platform.

Your products must also comply with Section B.5 of the Shopify Payments terms of service, on prohibited items. Shopify's prohibited list names prescription drugs and medical devices among regulated products, plus pseudo pharmaceuticals with unverified health claims, and the list varies depending on your region. If you aren't eligible for Shopify Payments, you can add a third-party payment provider instead.

Why do FSA and HRA cards get declined at online stores?

IRS Notice 2006-69 lets a health FSA or HRA card pay at merchants with healthcare merchant category codes (MCCs), or at stores whose card processor approves each item by SKU through an inventory information approval system (IIAS). Notice 2007-2 turned that into a hard rule for stores without a healthcare code:

Under IRS rules, that leaves three ways to accept these cards:

• IIAS — the route left for a store without a healthcare code: it flags eligible items using the SIGIS Eligible Product List.
• Healthcare MCC — physicians, dentists, vision care offices, hospitals and other medical care providers.
• The 90 percent rule — an IRS test separate from Shopify's 90% condition, only for the Drug Stores and Pharmacies MCC, measured location by location on prior-year gross receipts.

Under IIAS a mixed cart becomes a split-tender transaction: the card covers the eligible items, the shopper pays the rest, and no receipt is needed. Visa names a non-IIAS/SIGIS-certified merchant as a typical reason its FSA and HRA cards are declined, and SIGIS notes that IIAS doesn't guarantee every FSA/HRA card is accepted. Both IRS notices name health FSA and HRA cards, not HSAs.

Which apps add HSA and FSA payments to a Shopify store?

These are the HSA/FSA listings we found on the Shopify App Store on October 18, 2026 — a snapshot, not a ranking or a complete list. Only the first column takes the card at checkout; the second is reimbursement after the purchase:

Before you install, check three things:

• The vendor accepts your store — Flex's listing says it serves merchants that qualify.
• The vendor's terms — Truemed refers pricing to its enterprise merchant agreement.
• Health data — Truemed's flow runs a health intake survey where needed, and Shopify's Acceptable Use Policy says uploading Protected Health Information subject to HIPAA isn't supported on the platform — see what to do with customer health data.

Who decides which products are HSA or FSA eligible?

The benefit plan sets the rules; apps such as Flex and Truemed apply them product by product. IRS Publication 969 (2025) says qualified medical expenses are those specified in the plan that would generally qualify for the medical expense deduction. For an FSA, over-the-counter medicine (whether or not prescribed) and menstrual care products count, and an IRS release on the CARES Act says both are reimbursable from HSAs too, for amounts paid after December 31, 2019. Publication 502 adds that medical expenses don't include items merely beneficial to general health, such as vitamins.

Flex assigns eligibility under §213(d) down to each product's UPC or GTIN; Truemed Extensions keeps eligibility in sync with your SKUs, and anything Truemed hasn't finished reviewing is ineligible. Mark nothing as eligible until the app's review is done.

Flex says products without direct eligibility need a Letter of Medical Necessity (LMN) from a physician; Truemed says it issues one within 24–48 hours if the shopper is eligible.

Following your partners' rules and the law stays your job under Shopify's Acceptable Use Policy.