Tagada
Ecommerce OS · Supplements5 min readUpdated October 26, 2026

Shopify Checkout for Supplement Brands

What a supplement brand can and can't do in Shopify checkout in 2026: payments, subscriptions, upsells, tracking after the script sunset.

Nick Bonnassies, CMO at Tagada · checked against 8 sources

Article summary

TL;DR

Shopify's checkout is fast and trusted, but for a supplement brand it has three limits: one card processor at a time, a 0.2% to 2% fee if that processor isn't Shopify Payments, and customizations only through Shopify's extensions since the old scripts were retired. Keep Shopify checkout if Shopify Payments accepts you and you need little customization; add a separate checkout layer if you need your own processors, a backup, or deeper funnels.

  • Shopify allows one credit card processor at a time; a third-party processor costs 2% (Basic) down to 0.2% (Plus) per order.
  • Shopify Payments applies its processors' prohibited lists; Stripe restricts nutraceuticals that are unsafe or make harmful claims.
  • Script tags on the Thank you and Order status pages were sunset on August 28, 2025 for Plus stores and on August 26, 2026 for other plans.
  • Checkout customizations now go through checkout UI extensions and Shopify Functions.
  • Shopify Subscriptions supports a limited list of gateways.
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On this page

This guide is part of our playbook on the best ecommerce platform for supplement brands. The broader choice is in Shopify or a sales funnel for your supplement brand.

What changed in Shopify checkout

DateChangeWho
August 13, 2024checkout.liquid retired for the information, shipping and payment stepsPlus stores7Braze, Shopify checkout deprecation notes, read October 26, 2026 (secondary source)
August 28, 2025checkout.liquid, additional scripts and script tags retired on Thank you and Order status pagesPlus stores1Shopify.dev, Apps in checkout, read October 26, 2026
August 26, 2026Script tags retired on Thank you and Order status pagesNon-Plus stores1Shopify.dev, Apps in checkout, read October 26, 2026

What replaced them: checkout UI extensions, Shopify Functions, branding settings and web pixels1Shopify.dev, Apps in checkout, read October 26, 2026.

Fig. 1The script sunset, step by step

  1. August 13, 2024Plus: checkout.liquid retired on information, shipping and payment
  2. August 28, 2025Plus: scripts retired on Thank you and Order status
  3. August 26, 2026Non-Plus: script tags retired on the same pages
  4. NowCheckout UI extensions, Shopify Functions, web pixels

Since August 26, 2026, every plan is on extensions.

Shopify.dev, Apps in checkout; Braze, Shopify checkout deprecation notes.

Watch out

Tracking or upsell code that lived in "Additional scripts" stops without an error message. Orders keep coming in while your ad platforms stop receiving them. Check your purchase events if you haven't since August 2026.

What a supplement brand can and can't do

NeedIn Shopify checkoutNote
Use Shopify PaymentsYesIf your products fit its processors' rules4Shopify Payments Terms of Service (US), read October 9, 2026Supplements reviewed more closely
Use your own processorYesOne card processor at a time2Shopify Help Center, Configuring third-party payment providers, read October 26, 2026Plus a 0.2% to 2% fee3Shopify pricing, third-party payment provider fees, read October 26, 2026
Backup processor and cascadeNoOne card processor at a time2Shopify Help Center, Configuring third-party payment providers, read October 26, 2026Needs a separate checkout or payment layer
Order bumpsThrough apps using checkout extensionsCheck plan availability
Post-purchase upsellsThrough apps using post-purchase or Thank you extensionsCheck plan availability1Shopify.dev, Apps in checkout, read October 26, 2026
SubscriptionsShopify Subscriptions or apps; limited gateways5Shopify Help Center, Shopify Subscriptions considerations, read October 9, 2026Check your processor is supported
Server-side trackingWeb pixels plus a server-side setupOld scripts no longer run1Shopify.dev, Apps in checkout, read October 26, 2026

Payments in Shopify checkout

Fig. 2Shopify's fee on a third-party card processor, by plan

  1. Basic2%
  2. Grow1%
  3. Advanced0.6%
  4. Plus0.2%

Source: Shopify pricing, third-party payment provider fees, read October 26, 2026

Per order, on top of the processor's own fees.

Fig. 3Same declined card, two checkouts

Shopify checkout

  1. CheckoutOne card processor
  2. routes toProcessorDeclined or account pausedDeclined

Card payments stop until you switch

Checkout layer with routing

  1. CheckoutSeveral processors connected
  2. routes toProcessor ADeclinedDeclined
  3. falls throughProcessor BCascade on declineApproved

Order paid, orders synced to Shopify

Illustrative path.

Routing between several processors needs a checkout or payment layer outside Shopify's: see payment routing and backup processors.

Subscriptions and upsells on Shopify

  1. Shopify Payments

    Supported by Shopify Subscriptions.

  2. PayPal Express

    Supported by Shopify Subscriptions.

  3. Authorize.net

    Supported, with no Apple Pay or Google Pay there.

  4. Adyen

    Supported by Shopify Subscriptions.

  5. Stripe

    "Available only to select merchants".

  • Upsells: post-purchase and Thank you page offers run through apps built on Shopify's checkout extensions1Shopify.dev, Apps in checkout, read October 26, 2026.
  • One system for renewals: if you add an outside checkout for some traffic, decide which system renews subscribers.

More: subscription billing and one-click upsells for supplement brands.

Tracking after the script sunset

  1. List what used to run in Additional scripts and checkout.liquid.
  2. Move browser tracking to web pixels supported by Shopify1Shopify.dev, Apps in checkout, read October 26, 2026.
  3. Add server-side purchase events for Meta, Google and TikTok, with the same event ID as the browser event8Meta for Developers, Deduplicate Pixel and server events, read October 26, 2026.
  4. Compare store orders with ad platform purchases for two weeks.

Run it if you haven't checked your purchase events since August 2026.

Details: server-side tracking for supplement brands.

Keep Shopify checkout, or add a checkout layer?

Your situationChoice
Shopify Payments accepts you, simple offersKeep Shopify checkout
Your own processor, no backup neededShopify checkout with one third-party processor, and its fee
Need a backup processor or routingA checkout layer that supports several processors
Funnels with bumps, upsells and A/B tests on paid trafficA checkout layer for that traffic, orders synced to Shopify
Subscriptions on a processor Shopify Subscriptions doesn't supportA subscription system on a checkout that supports it

How Tagada helps

A checkout and payments layer on top of Shopify

Tagada runs on Shopify as a checkout and payments layer, or standalone:

  • Checkout: one page, Apple Pay and Google Pay, order bumps, one-click upsells, A/B tests
  • Payments: routing across Stripe, Adyen and TagadaPay, with cascade on decline
  • Subscriptions: trials, billing cycles, retries and automatic recovery
  • Tracking: server-side events to Meta, Google and TikTok

Plans are on the pricing page.

Start free
A checkout and payments layer on top of Shopify

Updated on October 26, 2026

Nick Bonnassies

CMO at Tagada

CMO at Tagada. Before Tagada, Nick built direct-to-consumer brands that generated over $115M in sales, raised over $25M in crowdfunding and sold two of them. He also works as a fractional CMO on marketing operations and AI systems.

Frequently asked questions

Can I sell supplements with Shopify checkout?

Yes. Shopify checkout works with Shopify Payments, whose processors' prohibited lists apply, or with one third-party card processor, which adds a 0.2% to 2% fee per order depending on your plan.

Can I use two payment processors in Shopify checkout?

Not for cards: Shopify allows one credit card processor at a time. PayPal and some alternative methods can run alongside it. For a card backup or routing, you need a checkout or payment layer outside Shopify's own.

What happened to Shopify checkout scripts?

checkout.liquid and additional scripts were retired, and script tags on the Thank you and Order status pages stopped on August 28, 2025 for Plus stores and on August 26, 2026 for other plans. Customizations now use checkout UI extensions, Shopify Functions and web pixels.

Does Shopify Subscriptions work with any processor?

No. It supports a limited list: Shopify Payments, PayPal Express, Authorize.net, Adyen and Stripe, the last "available only to select merchants". Check your processor before you plan subscriptions on Shopify.

Sources

Checked October 26, 2026
  1. Shopify.dev, Apps in checkout, read October 26, 2026
  2. Shopify Help Center, Configuring third-party payment providers, read October 26, 2026
  3. Shopify pricing, third-party payment provider fees, read October 26, 2026
  4. Shopify Payments Terms of Service (US), read October 9, 2026
  5. Shopify Help Center, Shopify Subscriptions considerations, read October 9, 2026
  6. Stripe, Prohibited and restricted businesses, read October 9, 2026
  7. Braze, Shopify checkout deprecation notes, read October 26, 2026 (secondary source)
  8. Meta for Developers, Deduplicate Pixel and server events, read October 26, 2026

Tagada

Need more than one processor behind your Shopify store?

Funnels, one-click upsells, subscription billing and payment routing, on one customer record.

Start freeSee pricing
  1. 01Create your free account
  2. 02Connect your store or build a checkout
  3. 03Launch funnels, upsells and subscriptions