How do we migrate active subscription contracts (Recharge, Skio, or native Shopify Subscriptions) from one Shopify store to another during consolidation?

Why is moving subscriptions between two Shopify stores harder than it looks?

Moving subscriptions between two Shopify stores is harder than it looks because each store keeps its own saved payment methods. Shopify says each store in a Plus organization "operates completely independently with its own separate data, settings, and configurations" (Shopify Help Center, October 2026). The contract data is the easy part, because it moves by export and import. The card behind each contract is the hard part, so a consolidation follows the payment-first sequence for migrating an active subscription program. One thing differs: Shopify's secondary-gateway route serves Stripe, Braintree, PayPal Express and Authorize.net, not Shopify's own vault (shopify.dev, October 2026). Deploi's cross-store accounts record reads the same store boundary for shopper accounts and order history (October 2026).

Where can a subscriber's saved payment method sit, and what moves it?

A subscriber's saved payment method sits in Shopify Payments, Shop Pay, a legacy gateway or PayPal, and where it sits decides whether any route reaches the destination store.

So count subscribers by place before you plan anything else. Which saved payment methods break when the account behind them changes has its own answer.

What do Recharge, Skio and Shopify Subscriptions each do with the contracts?

Recharge, Skio and Shopify Subscriptions each recreate the contracts in the destination store, and each needs the payment methods there first.

• Recharge: you export the subscriptions, update product, variant and payment method IDs for the new store, then import. Recharge warns that a store move "changes product, variant, customer, and subscription IDs" and that historical analytics and reporting don't transfer (Recharge store-to-store guide, October 2026). Recharge Support doesn't run the migration for you.
• Skio: its migrations team runs the move once Skio is installed on the source store, customers are imported into the destination and a variant-mapping file is filled in. Skio quotes 1 to 3 weeks that "cannot be expedited" and can't move Prepaid gift subscriptions (Skio store A to store B guide, October 2026). Skio then cancels the source store's subscriptions silently, so run Skio's subscriber and consent exports first.
• Shopify Subscriptions: contracts export as a comma-separated values (CSV) file for another store with the app installed (Shopify Help Center, October 2026). The import rejects any payment method ID that doesn't match one in the destination admin (Shopify's CSV troubleshooting page, October 2026).

What should you settle before the consolidation case is signed?

Settle three answers before the consolidation case is signed, because each one moves the expected subscriber loss.

1. Where each subscriber's payment method sits, counted by place: Shopify Payments, Shop Pay, a legacy gateway or PayPal. Plan the Shop Pay count as a re-collection campaign. Plan the PayPal count the same way unless your app developer confirms its import flow supports your PayPal account.
2. Shopify's written answer on the card move, naming the stores and the cards. Shopify's page gives its paid Professional Services migration as the route for a consolidation (Shopify Help Center, October 2026).
3. What a contract with no payment method does. Shopify's billing attempt fails by default when no valid payment method exists (shopify.dev billing attempt reference, October 2026). An app can instead skip payment and create an unpaid order to collect by hand (shopify.dev processing policy reference, October 2026).

Pause billing in the source store's app while payment methods and contracts move: Shopify "strongly recommend[s]" it, to avoid double-billing a contract (shopify.dev, October 2026). Deploi's subscription migration record runs both platforms for 2 to 4 weeks (October 2026). Use that overlap to compare dates and amounts, with each subscriber billing on one store at a time. Keep the source store open until the last contract has billed from the destination. The retiring store's draft orders and open carts need their own cutover plan.

When is consolidating the subscriptions the wrong move?

Consolidating the subscriptions is the wrong move when store structure solves the problem for less than a merge costs in subscribers.