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This guide assumes you’ve already created your Flex account and added your payout information. Complete that first if you haven’t.
Flex uses two Shopify apps, and your store needs both for HSA/FSA checkout. Connecting your store from the Flex Dashboard installs the first one for you. You install the second from the same page once your products start syncing.

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Installation guide

1

Connect your Shopify store from Flex

In the Flex Dashboard, navigate to Settings → Integrations → Shopify.Under Connection, enter your Shopify store subdomain (e.g., your-store for your-store.myshopify.com) and click Connect.The Connection section of the Shopify integration page, with a store subdomain field and a Connect buttonYou’ll be redirected to Shopify Admin to approve the permissions for Flex Extensions (formerly Flex Marketing). This is the first of the two apps. Approving it installs the Flex pixel, starts product sync, and lets Flex push HSA/FSA eligibility back to your catalog.Once approved, Shopify sends you back to Flex. The pixel installs automatically and product sync begins.The Connection section showing Syncing Products, with Flex Extensions connected under Apps
Product sync can take several minutes or longer depending on the number of products in your store. You can leave the page. Sync continues in the background and the dashboard updates when it’s done.
When sync completes, your store shows as Connected.The Connection section showing the store Connected, with Flex Extensions connected under AppsFlex Extensions also provides the storefront blocks for eligibility badges, landing pages, and checkout messaging. See Flex Extensions to set those up once you’re live.
2

Sync products & eligibility

Flex syncs the products from your Shopify store and creates a corresponding product in Flex. We also configure a webhook that listens for any product changes on your Shopify store.Once synced, Flex will automatically determine HSA/FSA eligibility for all products using an intelligent multi-stage pipeline and categorize products into the following eligibility types:
3

Install the Shopify Flex Payments app

Once your products start syncing, go back to Settings → Integrations → Shopify in the Flex Dashboard. Under Apps, find Flex Payments and click Install. This is the app that shows Flex as a payment method at checkout.The Shopify integration page with Flex Extensions connected and an Install button next to Flex PaymentsYou’ll be redirected to Shopify Admin to approve its permissions, the same way you did for Flex Extensions.
4

Configure Flex as a payment gateway on your store

In Shopify Admin, navigate to Settings → Payments and verify that “Pay with Flex” is set to ‘Active’.If you do not see “Pay with Flex,” select Add payment method and search for Flex.
5

Confirm Flex checkout functionality

Navigate to Settings and select Customer Events to verify the Flex Pixel status is ‘Connected’.Verify the checkout is working by adding a product to the cart and selecting ‘Pay with HSA/FSA’ at checkout. You should be redirected to the Flex Checkout to enter payment details.
6

You're all set

Both apps are installed. Flex Extensions is syncing your products and eligibility, and the Shopify Flex Payments app is handling HSA/FSA payments at checkout.
If your store doesn’t show as Connected, contact merchanthelp@withflex.com.

Set up your storefront with Flex Extensions

Flex Extensions is already installed from step 1. Use its theme blocks to add eligibility badges to your product pages and build an HSA/FSA landing page.