Shop Pay quietly added a "Pay another way" option at checkout. Here is what changed, why it matters for HSA/FSA conversion on Shopify, and what merchants on Shop Pay should do about it.
Overview
For a shopper logged into Shop Pay, the fastest checkout in the store has historically been one that couldn’t support HSA/FSA payments through Flex. Shop Pay is an accelerated checkout that loads a user’s saved information, including addresses and payment details, but it was not available to third-party payment options. To use Flex, that shopper had to abandon their saved profile, drop to a guest checkout, and re-enter information they had already stored.
Shopify now supports Shop Pay with a “Pay another way” option for Flex merchants. From Shop Pay, shoppers can select “Pay another way” to choose a third-party payment option like Flex, while still using their saved information. The re-entry tax is gone. For merchants whose volume rides heavily on HSA/FSA, removing that step sits directly on the path to a completed order.
This is a Shopify-side change to the checkout dropdown, not a Flex code release, so there's nothing for you to deploy. But it's worth understanding exactly what changed, why it matters for your conversion, and what you can do to point shoppers at it.
What “Pay another way” changes in the Shop Pay flow
The difference between the old flow and the new one is simple.
Before, a shopper logged into Shop Pay had to re-enter their information to use Flex. Now, they can select “Pay another way” and still use their saved details.
Instead of starting from a blank checkout, their phone, name, and shipping address are already filled in. What used to take multiple steps now feels like a single tap.
That small change removes friction at a critical moment in checkout and makes it much easier for shoppers to complete their order with HSA/FSA.
Why this matters for your store
HSA/FSA isn’t a side payment method for most Flex merchants, it’s the reason the order exists. Across our top partners, HSA/FSA-eligible spend regularly dominates GMV. When a primary payment method sits behind a re-entry wall, every extra step costs orders.
Those orders convert, too. Flex checkout sessions for the highest-volume merchants run at roughly 50% to 54%. An upstream Shop Pay drop-off, a logged-in shopper who bounces rather than re-enter their address, is a drop-off against that ~50% base, not against zero.
And Shopify is a high-volume surface for this flow. Flex-on-Shopify checkout sessions run around 1K+ per day in steady state and peaked at 9K+ during the holiday rush. At that scale, a smoother path isn’t a rounding error.
What Flex merchants on Shopify should do now
There’s no Flex deploy required, the option appears in Shop Pay’s dropdown. The useful moves are on the merchant and communication side:
- Point your HSA/FSA-eligible shoppers to the “Pay another way” option directly, in product education, support macros, and at the moment of checkout confusion. The most common HSA/FSA support ticket is “how do I pay with my card here?” and the answer just got shorter.
- Lean into the broader Shopify story while you're at it. If you're not yet set up to accept HSA/FSA on your Shopify store, this lowers the friction on the single most-used path to doing so.
- Make sure your shopper-facing education covers the basics, what HSAs and FSAs are and, for anyone who still misses the option at checkout, the HSA reimbursement path as a fallback. The IRS sets which expenses qualify (Publication 502).
