Migrating from Recharge to Shopify Native Subscriptions: The Zero‑Churn Checklist

Subscriptions are the lifeblood of many e‑commerce brands. A recurring revenue model delivers predictable cash flow and customer loyalty — but the tools you use to manage those subscriptions can make or break your margins. Recharge to Shopify migration has long been the subscription platform for Shopify stores. Yet its steep monthly fees and per‑order transaction charges (starting at US$99 per month plus 1.49 % + 19 ¢ per order) leave many brands looking for alternatives. Shopify’s native subscriptions (introduced in 2024) offer a no‑subscription‑fee solution with tight integration into the Shopify admin, but migrating thousands of active subscribers can feel risky. What happens to legacy payment tokens and credit cards? Will customers be forced to re‑enter details? How can you avoid churn during migration?

This guide provides a zero‑churn migration checklist for moving from Recharge to Shopify Subscriptions. By leveraging custom scripts and Shopify’s CustomerPaymentMethodRemoteCreate and subscriptionContractAtomicCreate APIs, you can keep customers’ payment data intact and ensure a seamless transition. We’ll cover why businesses switch, the challenges around payment tokens, and step‑by‑step instructions for a safe migration. We’ll also link to our guides on common Shopify website mistakes and e‑commerce development services to help you optimise your store once the migration is complete.

Why Migrate? The Cost of Staying on Recharge

Recharge is popular because it predates Shopify’s native subscription offering and offers a rich feature set. However, the cost difference is dramatic. Recharge’s Starter plan starts at US$99 per month plus 1.49 % + 19 ¢ per transaction, while its Pro plan costs US$499 per month plus 1.25 % + 19 ¢ per transaction. In comparison, Shopify Subscriptions is free (aside from standard payment gateway fees). For brands processing tens of thousands of subscription orders, those percentage fees alone can add up to US$5 k or more every month. Subscriptions also create tech debt: maintaining external APIs, handling webhooks, and dealing with separate dashboards increases operational complexity. Shopify’s native solution consolidates subscription management in the same admin used for product, order and customer management — lowering overhead and risk.

Cost is not the only driver. Many merchants find Recharge’s management interface and API limiting or overly complex for custom workflows, especially when integrating with CRM or ERP systems. If you plan to implement advanced personalisation or offer dynamic bundles, you may need a more open platform. Shopify’s native API gives you control over subscription contracts, billing schedules and payment methods; plus it integrates directly with Shopify Flow for automated workflows.

The Big Hurdle: Migrating Payment Tokens

The greatest fear when leaving Recharge is losing your subscribers’ payment methods. If customers have to re‑enter their card details, many will lapse — causing immediate revenue loss. Unfortunately, migrating payment tokens isn’t as simple as exporting a CSV. Recharge cannot move the payment token from your current payment processor to Shopify Payments; instead you must use Shopify’s Payment Migration Services or handle token import yourself. Additionally, some token data is stored with the payment processor, so you need to export payment tokens from Recharge and possibly contact your gateway.

To prepare, follow these steps:

1. Export all relevant data from Recharge. The Recharge export portal provides Customers – payment tokens, Subscription, Customer, and Orders reports. These CSVs will be the basis for mapping subscriptions into Shopify. Make sure to generate the payment token export; without it you cannot restore the legacy card details.

2. Identify your payment gateway. If you process cards via Stripe, Braintree or another gateway supported by Shopify, you may be able to use the CustomerPaymentMethodRemoteCreate mutation. This GraphQL mutation imports a remote payment method into Shopify by referencing the external payment method token (for example, Braintree’s paymentMethodToken). Only credit cards and Apple Pay can be migrated, and you must request token migration assistance from your payment processor if the tokens aren’t stored within Recharge.

3. Reconcile expired or missing tokens. Recharge notes that expired payment methods may not migrate. Customers with expired cards will need to re‑enter their payment details once the migration is complete. You can segment these customers and send targeted communication reminding them to update their cards.

Mapping Recharge Data to Shopify Subscriptions

Shopify’s subscription architecture is based on two core objects: Customer Payment Methods and Subscription Contracts. A migration must create both before the first billing cycle. Here’s how to map Recharge data to the Shopify equivalent:

1. Import customers and payment methods

Start by creating or updating the customer record. Use the CustomerPaymentMethodRemoteCreate mutation to import each customer’s payment method. The mutation accepts parameters such as customerId, vaultProvider (e.g., BRAINTREE or STRIPE), remoteReference and type (e.g., CARD). In the remote reference, set paymentMethodToken or a similar field (depending on the gateway) to the value exported from Recharge. The API will return a paymentMethodId representing the vaulted card in Shopify.

If your payment gateway doesn’t support token migration or the token is missing, you can create a customer without a payment method. Customers can then add a new card through an email prompt or on their account page. Once added, you can attach the new payment method to the subscription contract using customer_payment_methods/create webhooks.

2. Create subscription contracts

Next, map each subscription line item. A subscription contract in Shopify includes the customer, the product variant, the selling plan, billing interval, shipping and billing addresses, and the paymentMethodId. Use the subscriptionContractAtomicCreate mutation to create the contract. Provide the variant ID and plan ID (matching the frequency from Recharge), and set paymentMethodId to the ID returned from CustomerPaymentMethodRemoteCreate. Shopify’s API ensures that billing continues seamlessly for the next cycle. You can optionally omit the payment method during contract creation and attach it later before the first charge.

3. Schedule the migration during a quiet period

To minimise disruption, schedule your migration during a low‑traffic window (e.g., overnight). Pause new subscriptions in Recharge and disable subscription checkout on your live storefront. Then run your migration scripts to import customers, payment methods and contracts. After verifying data integrity (including subscription status, next billing date and item quantities), switch your storefront to Shopify Subscriptions and point renewal notifications to Shopify. Reactivate subscription checkout using Shopify’s selling plans.

4. Communicate with your customers

Transparency prevents churn. Inform subscribers of the upcoming migration, emphasising that no action is required unless their card has expired. For customers with missing or expired tokens, send personalised emails requesting updated payment information. Use Shopify Flow or Klaviyo to trigger reminders automatically.

5. Decommission Recharge and reconcile accounting

After verifying that all recurring charges are processing correctly, cancel your Recharge subscription. Remove the Recharge app from your Shopify admin and check that webhooks are no longer firing. Update your accounting records to reflect the change in fee structure and reduced subscription costs. Use analytics to compare churn rates before and after migration; an effective zero‑churn migration should show minimal drop‑off.

Handling Edge Cases: Subscriptions, Discounts and Metafields

Some subscriptions may include additional complexity, such as:

• Discount codes and free trials. If a subscription has discount codes applied in Recharge, you can replicate these in Shopify by creating a corresponding discount code and referencing its ID when creating the subscription contract. Shopify Functions or Flow can handle complex discount logic.

• Metafields and custom properties. Recharge stores extra fields (e.g., gift messages or internal notes) as properties on line items. Shopify also supports metafields on subscription contracts; you can map these properties into contract metafields with the appropriate namespace and key. This ensures you don’t lose custom data during migration.

• Prepaid or pay‑as‑you‑go subscriptions. Recharge supports prepaid cycles (e.g., pay for 12 months and ship monthly). Shopify Subscriptions can replicate this by creating selling plans with the same billing and delivery intervals.

Conclusion: A Zero‑Churn Migration Is Possible

Migrating from Recharge to Shopify Subscriptions may seem daunting, but with careful planning and the right API strategies you can avoid disruptions. By exporting payment tokens and using Shopify’s CustomerPaymentMethodRemoteCreate to import them, then creating subscription contracts via subscriptionContractAtomicCreate, you maintain customers’ active payment methods and avoid forcing re‑entries. Remember to communicate with customers, schedule during off‑peak hours, and monitor for any anomalies.

Recharge’s high fees and separate management interface are pushing more brands toward Shopify’s native solution. With a well‑executed migration, you’ll enjoy a more unified platform, lower operating costs, and the peace of mind that your subscribers remain intact. If you need help with a custom migration script or want to audit your existing subscription setup, our team offers a free tech stack audit — get in touch to ensure your migration is truly zero churn.