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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.

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Installation guide

1

Connect your Shopify store from Flex

In the Flex dashboard, navigate to Settings → Integrations → Shopify.Enter your Shopify store subdomain (e.g., your-store for your-store.myshopify.com) and click Connect.You’ll be redirected to Shopify Admin to approve the Flex app’s permissions.Once approved, Shopify sends you back to Flex. The pixel installs automatically and product sync begins.
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 and is ready to use.
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

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.
4

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.
5

You're all set!

You have successfully installed the Flex Shopify Payments App and enabled Flex Shopify Payments on your store.
If your store doesn’t show as Connected, contact merchanthelp@withflex.com.

Install the Flex Marketing App

Promote HSA/FSA across your storefront with dynamic badges, a prebuilt landing page, and product eligibility synced from Flex.