Shopify Stripe integration and Square integration: what's possible

A Shopify Stripe integration is usually one of three things: using Stripe-held payment data in Shopify (for example moving subscriptions), connecting Stripe-billed revenue to the same reporting as Shopify, or reconciling payouts from several providers. A Square Shopify integration usually means keeping a Square POS in a physical shop in sync with an online Shopify store. What you can't do is plug your own gateway into Shopify checkout with custom code, and it's worth knowing that before planning a project.

Payments at Shopify checkout: the rules

• Checkout payments go through Shopify Payments or a third-party payment provider that Shopify supports in your country. Which providers are available is shown in your Shopify admin under Settings > Payments.
• New payment providers integrate through Shopify's Payments Apps API, which is invitation-only for approved payment partners. A merchant or freelance developer can't write a custom gateway for their own store.
• What you can customise with code is which payment methods show and when, with a Payment Customization Shopify Function: hide, reorder or rename methods by cart, customer or market. Some limits apply. Methods shown as logos, such as wallets, can't be renamed, and hiding individual placements is Plus-only.
• Using a third-party provider can bring extra fees on some plans. The profit margin calculator lets you enter your own rates to see the effect per order.

Stripe: the integrations that make sense

Moving subscriptions from Stripe to Shopify

If you ran subscriptions on Stripe Billing, next to or before Shopify, you can move them into Shopify's native subscription model:

1. Import customers into Shopify.
2. Import their Stripe payment methods as remote references with the customerPaymentMethodRemoteCreate mutation. Cards stay in Stripe's vault and don't pass through your servers.
3. Create selling plans matching your subscription offers, and recreate each subscription as a subscription contract.
4. Pause billing in Stripe while you migrate, to avoid double charges, then switch billing to Shopify.

Shopify's documentation describes this for Stripe, Braintree, PayPal Express and Authorize.net. Subscription contracts can now be created through the API without a payment method attached, so contracts with missing or expired cards can move first and have their payment details collected later.

Stripe for payments outside the store

Many merchants use Stripe for things that aren't Shopify orders: B2B invoices from another system, event tickets, services, deposits. A custom integration can:

• create Shopify orders or customer records from Stripe events (via Stripe webhooks), when you want one view of the customer;
• send both Stripe and Shopify revenue to accounting with the same mapping;
• reconcile Stripe payouts next to Shopify Payments payouts.

Reconciling several providers

Each provider has its own payout schedule, fees and refund timing. In accounting, give each provider its own clearing account: Shopify Payments, PayPal, Stripe and marketplaces. Post sales and fees against it, and post payouts from it to the bank. The QuickBooks and Xero guides describe this model.

Square: POS and online in sync

The common set-up: physical shops on Square POS, online store on Shopify, one shared stock pool.

What needs to sync

• Catalog: products and variants with a shared SKU as the key. Pick one system as the master for product data.
• Inventory: sales in either system reduce the shared stock. Each Square location maps to a Shopify location, or shares one pool.
• Orders (optional): Square sales copied into Shopify, or both into accounting, for unified reporting.
• Customers (optional): a single customer record across channels. This is the hardest part to get right.

Off-the-shelf: connector apps on the Shopify App Store sync Square and Shopify products and inventory. Check how they handle variants, multiple locations and sync frequency.

Where it breaks

• SKU mismatches or duplicate SKUs across the two catalogs.
• Stock races: the last item sells in the shop and online within seconds.
• Variant structures that differ between Square items and Shopify products.
• Refunds and exchanges made in-store on items bought online, or the reverse.

Custom integration design

1. Square webhooks (inventory and catalog changes, payments) and Shopify webhooks (orders/create, inventory_levels/update, products/update) both feed a queue.
2. A mapping table links Square catalog object IDs to Shopify variant IDs, keyed on SKU.
3. Inventory changes are applied as adjustments in the other system rather than absolute overwrites, and a periodic full recount corrects drift.
4. Every event is processed idempotently, keyed on the source system's event or object version, so replays don't double-count.

Worked example: one day, three providers

Imagine a store taking Shopify Payments and PayPal online, and Square in its shop:

1. Sales post daily per provider: Shopify Payments sales to the "Shopify Payments clearing" account, PayPal sales to "PayPal clearing", Square sales to "Square clearing".
2. Fees post against the same clearing accounts when each provider reports them.
3. Payouts arrive on different days. Each one posts as a transfer from its clearing account to the bank, and matches the bank line exactly.
4. Refunds reduce the clearing account of the provider that refunded, whichever day that happens.
5. At month-end, each clearing account's balance equals money in transit: sales not yet paid out. Anything else is a problem to investigate.

The integration's job is to produce these entries automatically and to flag any payout whose parts don't add up.

Decision checklist

• Is the goal payments at checkout (limited to supported providers), subscriptions, reporting or POS sync?
• Which payment providers and payout currencies are involved?
• For Square: which system is the product master? How many locations?
• Would moving to Shopify POS remove the need for the integration?