Shopify ↔ Stripe: Payment Processing & Refund Sync
If you process Shopify orders through Stripe, you need to sync refunds back to Shopify, track disputed chargebacks, and reconcile accounting. This guide covers native integration, Zapier, and n8n approaches.
Quick Answer
Shopify's native Stripe app handles standard payment processing. Use Zapier ↗ to sync refunds and Make ↗ for chargeback workflows.
Why Sync Shopify and Stripe?
Stripe processes the payment but Shopify owns the order. When a customer requests a refund, Stripe records it but Shopify's order status stays "Paid" until you manually update it. Syncing automates this and flags fraud/chargebacks for review.
Method Comparison
| Factor | Native | Zapier | Make |
|---|---|---|---|
| Refund Sync | ✅ Automatic | ✅ Via webhook | ✅ Via webhook |
| Chargeback Alerts | ❌ No | ✅ Yes | ✅ Yes |
| Partial Refund Handling | ✅ Native | ⚠️ Manual | ✅ Automated |
| Setup Time | 5 min (1-click) | 30 min | 1–2 hours |
Method 1: Native Integration (Fastest Setup)
Shopify's native Stripe app is installed from the Shopify App Store. It handles all payment processing, and refunds in Stripe automatically sync back to Shopify orders as "Refunded" status.
What's Included
- Payment processing (full, partial refunds)
- Automatic refund status sync
- PCI compliance via Stripe
What's NOT Included
- Chargeback notifications
- Fraud flag sync (you see it in Stripe, but not in Shopify)
- Custom accounting reconciliation
Method 2: Zapier ↗ (Add Chargeback Alerts)
Keep the native integration for payment processing. Add a Zapier flow to monitor Stripe for chargebacks and disputes, then create a Shopify order tag or send a Slack alert.
Zap: Stripe Dispute → Shopify Alert
- Trigger: Stripe charge dispute created
- Action: Find corresponding Shopify order (by customer email + amount)
- Update order tag to "Disputed" or "Fraud Review"
- Send Slack message to #fraud-team with order details
Method 3: Make ↗ (Advanced Accounting Sync)
For teams that also sync to accounting software (QuickBooks, Xero), use Make to sync refunds, fees, and chargebacks to journal entries.
- ✓ Refund reconciliation — sync Stripe refunds to accounting software GL
- ✓ Fee tracking — record Stripe processing fees as a separate GL account
- ✓ Chargeback liability — create reversing journal entry when dispute is won/lost
Troubleshooting
Refund in Stripe But Not Synced to Shopify
Native app may not be syncing or webhook failed.
Fix: Check Shopify > Settings > Payments > Stripe webhook logs. Manually refund in Shopify admin to sync.
Partial Refund Amount Doesn't Match
Stripe fee or currency rounding issue.
Fix: Check if Stripe fee was refunded separately. Use Make to handle fee logic explicitly.