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Fix Stripe → Shopify Sync Issues (Not Working, Errors, Duplicates)

🔧 3 Common Issues

Diagnose and resolve common sync problems. We've documented the 3 most common issues, their root causes, and exactly how to fix them. See step-by-step fixes for duplicates, missing fields, rate limit errors, and connection issues.

critical High Frequency

Customer initiates refund in Stripe → Gets refunded → Files chargeback anyway → Shopify order still shows 'Paid'.

Also searched as: "Stripe Shopify customer initiates refund in stripe → gets refunded → files chargeback anyway → shopify order still shows 'paid'."

#1 One-Way Native Sync (Shopify → Stripe Only) 100% likely

📋 How to Diagnose

  1. 1. Native Shopify-Stripe integration: Shopify order data flows TO Stripe.
  2. 2. It does NOT listen for Stripe refunds, chargebacks, or payment status changes coming BACK to Shopify.

✓ Solution

Always initiate refunds in Shopify (Admin > Orders > Refund), not in Stripe Dashboard. If you must refund in Stripe, use Make to sync the refund status back to Shopify order.

⏱️ Est. time: 5 min

#2 Chargeback Data Lost (No Sync at All) 100% likely

📋 How to Diagnose

  1. 1. Stripe dispute resolved (customer loses chargeback).
  2. 2. Shopify order history shows ZERO record that a chargeback occurred.
  3. 3. Your accounting is missing a critical event.

✓ Solution

Use Make to listen for 'charge.dispute.closed' webhook from Stripe. Create a note or timeline entry in Shopify order with: dispute amount, outcome, date resolved.

⏱️ Est. time: 45 min

Use Make → →
View Setup Guide
high Very High Frequency

Weekly payout: Stripe Dashboard shows $10,050 transferred. Your Shopify order total shows $9,980. Missing $70. Where?

Also searched as: "Stripe Shopify weekly payout: stripe dashboard shows $10,050 transferred. your shopify order total shows $9,980. missing $70. where?"

#1 Fee Allocation Missing (Gross vs Net) 80% likely

📋 How to Diagnose

  1. 1. Stripe payout = Sales - Fees - Chargebacks - Refunds.
  2. 2. Shopify order total = Gross sales only.
  3. 3. Accountant doesn't see the fees broken out.

✓ Solution

Use Make to fetch payout details from Stripe API, break down fees + refunds per order, and attach to Shopify order timeline for full transparency.

⏱️ Est. time: 60 min

Use Make → →
View Setup Guide
high Moderate Frequency

Stripe transaction: $100 EUR. Shopify order page shows $118 USD (correct conversion). But accounting records show $100 USD anyway (missed the EUR symbol).

Also searched as: "Stripe Shopify stripe transaction: $100 eur. shopify order page shows $118 usd (correct conversion). but accounting records show $100 usd anyway (missed the eur symbol)."

#1 Currency Not Explicitly Tagged in Order Notes 85% likely

📋 How to Diagnose

  1. 1. Shopify order metadata has: {amount: 100, currency: 'EUR'}
  2. 2. But order display and export use: amount: 100 (no currency label).
  3. 3. Accountant assumes USD and records incorrectly.

✓ Solution

Use Make to append currency code to every Shopify order note: 'Order Total: 100 EUR (~$118 USD as of [date])'.

⏱️ Est. time: 20 min

View Setup Guide

Step 1: Try the Official Integration

Direct connection

Start with the native integration if available. It's usually the most reliable, but may have limitations.

View Setup Guide

Free with your subscription

Step 2: Use Make for Custom Flows

No code automation

Create custom integration workflows with Make's visual designer. It works with almost any API.

Try Make Free →

1000 ops/mo free. No credit card.

Step 3: Self-Hosted with n8n

Full data control

Need complete data privacy? n8n is open-source and self-hostable. Build custom integrations with full control over your data.

Try n8n Free →

Open source. Self-host or cloud. Unlimited ops.

Step 4: Add Human Review

Approval automation

Relay adds human-in-the-loop approvals, Slack/Teams alerts, and conditional logic to your automation.

Try Relay Free →

1000 actions/mo free. No credit card.