How to migrate customers to Shopify without losing loyalty points

Customer migrations fail quietly: the records arrive, the loyalty balances don't, and the first complaint comes from a top customer whose 12,000 points read zero. Shopify has no native points field, so a migration that preserves loyalty data has to decide where balances live and prove they arrived. This is the process.

Where loyalty data lives in Shopify

Customer metafields. A number_integer metafield such as loyalty.points_balance holds the balance; companion metafields hold lifetime value, tier, or join date. Metafields are readable from theme code (customer.metafields.loyalty.points_balance), checkout extensions, Shopify Flow, and any loyalty app you adopt later — which is what makes them the storage choice: the data outlives whatever reads it today.

Step 1 — validate the export before anything imports

Read the legacy export and reject problems while they're cheap: malformed emails, duplicate rows, missing balance fields, encodings that mangle names. Every record that enters the import clean is a record you don't reconcile by hand later. Duplicates deserve a decision, not a default — merge, skip, or flag, chosen per segment.

Step 2 — import in batches with tags and metafields together

One mutation creates the customer with segmentation tags and loyalty metafields attached:

mutation ImportCustomerWithLoyalty($input: CustomerInput!) {
  customerCreate(input: $input) {
    customer { id tags metafields(first: 5) { edges { node { namespace key value } } } }
    userErrors { field message }
  }
}

CustomerInput accepts metafields inline, so the balance is written in the same call that creates the record — no window where a customer exists without their points. Batch the file, record every userErrors response, and make the job resumable: a 40,000-record import will be interrupted at least once, and a rerun must not duplicate customers.

The customer CSV importer also accepts metafield columns, which covers a small clean file. Past a few thousand records, the API path wins on error reporting alone.

Step 3 — audit against the source

After the batches finish, reconcile: for each source row, fetch the customer and compare email, tags, and each metafield value against the file. Write mismatches to a report. The audit converts "the import ran" into a per-record account of what arrived and what needs follow-up — the same discipline as a subscription migration's verification pass.

Step 4 — connect the balance to something

A migrated balance nobody can see or redeem is a liability without a program. Point the storefront at the metafield — a balance display in the account area, a redemption path, or a loyalty app configured to read the imported values. The custom loyalty program guide covers the build that runs on these metafields directly.