You move subscriptions to Shopify in three parts: customers first, then their saved payment methods, then the subscription contracts. The data is the easy part. The saved cards decide who keeps paying, and they only move from gateways Shopify supports, such as Stripe, Braintree, PayPal Express and Authorize.net.
Below is what moves, what never moves, and the switch day plan we use so nobody is charged twice.
Key facts
- Shopify's developer docs name four gateways whose saved payment methods can move: Stripe, Braintree, PayPal Express and Authorize.net.
- From Stripe, only credit cards move. From Braintree, credit cards and Apple Pay move. PayPal and Google Pay saved in Braintree don't.
- Card security codes never move. PCI rules don't allow storing them after a payment.
- Subscriptions that bundle different products can't be migrated, according to Shopify.
- Shopify strongly recommends pausing billing in your old app during the move, so subscribers aren't billed twice.
- If your gateway isn't supported, cards must first move to one that is. Stripe says its imports usually finish within 10 business days after it gets valid data.
What moves to Shopify and what doesn't?
Every subscription is three records: the customer, the saved payment method, and the contract (product, price, interval, next charge). Each one moves differently.
- Customer details: Moves? Yes, How Imported first. Each record needs an email, a first name and a last name
- Cards saved in Stripe: Moves? Credit cards only, How The Stripe payment method ID is linked to the Shopify customer
- Cards saved in Braintree: Moves? Credit cards and Apple Pay, How The Braintree token is linked. PayPal and Google Pay are left behind
- PayPal billing agreements: Moves? Yes, if PayPal approves, How PayPal must approve your account for reference transactions
- Authorize.net profiles: Moves? Yes, How Both the customer profile ID and the payment profile ID are needed
- Card security codes: Moves? Never, How PCI rules forbid storing them
- Subscription contracts: Moves? Yes, How Through your new subscription app's import
- Bundles of different products: Moves? No, How Rebuild them as new subscriptions
- Past orders: Moves? Yes, separately, How With your store migration, not the subscription app
The pattern is simple. Shopify doesn't copy card numbers from your old store. It links the token your gateway already holds to the new Shopify customer. That is why the gateway decides everything.
Do subscribers have to enter their card again?
Not if the card sits in a supported gateway and the token links cleanly. Shopify ties the existing Stripe, Braintree or Authorize.net token to the customer, so the subscriber does nothing.
They do have to act in three cases:
- Your gateway isn't on Shopify's list, and the cards can't move to one that is.
- The card was saved as a wallet that can't move, such as PayPal or Google Pay inside Braintree.
- The token fails to link. Shopify's migration docs point to a separate tutorial for checking which payment methods imported and which were revoked.
For those subscribers, Skio's WooCommerce guide suggests an incentive to subscribe again on the new store. Plan that email before switch day, not after.
What if my gateway isn't supported?
Move the cards first. Stripe's Data Migrations team imports saved cards from another processor. You ask your old processor for an export, and Stripe imports it.
Two timings matter. Stripe says imports usually finish within 10 business days of receiving valid data. Your old processor's export can take anywhere from a few days to several months. So ask for the export the week you decide to move, not the week before launch.
Stripe also warns about one side effect. Your new account has a new merchant ID, so banks may decline more payments at first. Stripe suggests sending one-time and customer-initiated payments before recurring ones and growing volume step by step. For a subscription brand, that means watching the first renewals closely.
Which Shopify subscription app should I choose?
Pick the app whose team will run your import, then confirm your gateway with them in writing. Here is what the apps' own docs say about moving in.
- Shopify Subscriptions is Shopify's free app. It covers subscribe and save with weekly, monthly or yearly renewals.
- Loop says it migrates from non-Shopify platforms like WooCommerce, if the platform can provide the data. Its FAQ says a migration typically takes 3 to 7 working days.
- Skio has a WooCommerce guide. It tests payment methods first, then imports customers and maps products to subscription products.
All of them depend on Shopify's gateway rules. On Shopify, subscriptions run on Shopify Payments, PayPal Express, Authorize.net, Adyen and Stripe. Shopify notes that Stripe is available only to select merchants.
When we are not the right fit: your store is already on Shopify and you only want to change apps. The new app's migration team can do that without an agency.
What does a safe switch day look like?
The one rule: only one system bills at a time. These are the steps we follow.
- Six weeks out, check the gateway. List where every active card is saved. Start a card export now if any of them sit outside Shopify's list.
- Pick the app and get its plan in writing. Who runs the import, which gateways, how long, and what happens to cards that fail.
- Import customers. Each needs an email, a first name and a last name.
- Import payment methods. Check the import status for every one, and list the subscribers whose card didn't link.
- Import contracts with billing off. Skio's guide describes this. The new app holds the subscriptions but doesn't charge yet.
- Switch day. Turn off renewals in the old store, then turn billing on in the new app. Never both on at once.
- Run a last export. Catch anyone who subscribed during the switch, as Skio's guide advises.
- Email your subscribers. Tell them where to manage their subscription now, and ask the few with failed cards to add one.
Before you turn billing on, open 20 contracts by hand. Check the product, the price, the interval and the next charge date against the old store.
What should I check in the first two billing cycles?
Most problems show up on the first renewal, so check these on cycles one and two:
- Failed payments, compared with your normal rate on the old store
- Double charges, which mean the old system still billed someone
- Missed renewals, where a contract imported without a working payment method
- Wrong prices, most often old discounts that didn't carry over
- Support emails, which are the fastest early warning
From our work
We set up Loop subscriptions and Reviews.io in the custom theme we built for Qstar, a men's health brand. On PetsWorld, where we reworked the product page and the cart, Autoship & Save sits above the one-time purchase on the product page.
On a migration, subscriptions get their own line in the plan, with the gateway check done before the price is fixed. Our migrations start from $8,000, and we promise:
- "Your price doesn't move once you sign, unless the scope grows."
- "Your old store stays live until switch day."
- "If a redirect we set breaks in the first 90 days, we fix it free."
Frequently asked questions
Do subscribers have to re-enter their card when we move to Shopify?
No, if their card is saved in Stripe, Braintree, PayPal Express or Authorize.net and the token links. Shopify connects the existing token to the new customer. Subscribers on other gateways, or with wallets that can't move, need to add a card again.
Can next charge dates stay the same?
Yes. Each contract you import carries its own next billing date. Check a sample of contracts against the old store before billing goes live, because one wrong date column moves every renewal.
Which subscription app is best for supplements?
The one that supports your gateway and runs your import for you. We set up Loop for Qstar, a men's health brand. Shopify's free app covers simple subscribe and save. Ask each app about your gateway in writing before you choose.
Can the old store keep billing until the new one is live?
Yes, and it should. Import the contracts into the new app with billing off, then turn renewals off in the old store and on in the new app on the same day.
Planning the move?
If your store does $1M or more a year online, ask for the free Google traffic check. Within 2 business days you get your top Google pages, where each lands on Shopify, what breaks, and the fixed price in writing. Smaller stores can use the migration cost calculator and our migration cost guide.
Brands we build for: supplement brands and pet brands.
Sources
- Shopify, Migrate customer information to Shopify (opens in a new tab): gateways, payment method types, required fields, pausing billing.
- Shopify, Migrate to the Subscriptions API (opens in a new tab): bundles not supported. And Migrate subscription contracts (opens in a new tab): next billing date per contract.
- Shopify, Determine customer payment methods status (opens in a new tab): the tutorial the customer information page links for checking imported payment methods.
- Shopify App Store, Shopify Subscriptions (opens in a new tab): developer Shopify, pricing free.
- Shopify Help Center, Subscription considerations (opens in a new tab): gateways for subscriptions, Stripe for select merchants.
- Shopify Help Center, Shopify Subscriptions (opens in a new tab) and Setting up subscriptions (opens in a new tab): renewals, first‑party app.
- Stripe, Import payment data to Stripe (opens in a new tab): timings, security codes, new merchant ID.
- Loop, Migration FAQs (opens in a new tab): WooCommerce support, 3 to 7 working days.
- Skio, Migrating from WooCommerce to Shopify (opens in a new tab): billing kept off until switch day, a final export, and an incentive to subscribe again.
Facts checked November 10, 2026.
