Shopify Stripe Integration: Payment Processing Guide (2025)

Understanding Stripe’s relationship with Shopify is essential for optimizing your payment setup. This guide clarifies when to use Shopify Payments versus direct Stripe integration.

Shopify

integrates with

Stripe

Payments

Shopify Payments vs Stripe: The Relationship

Related: PayPal integration, the Shopify POS connector, convert image to favicon.

Here’s the key insight most merchants miss:

Shopify Payments IS Stripe.

Shopify Payments uses Stripe’s infrastructure, API, and payment processing. It’s a white-labeled Stripe solution optimized for Shopify merchants.

When to Use Shopify Payments

Use Shopify Payments when:

• You want the simplest setup
• Shopify Payments is available in your country
• You don’t need advanced Stripe-specific features
• You want to avoid additional transaction fees

Shopify Payments availability:

• United States, Canada, United Kingdom
• Australia, New Zealand, Ireland
• Germany, Austria, Netherlands, Belgium
• Spain, Italy, France, Singapore, Japan
• And more (check Shopify’s current list)

When to Use Direct Stripe Integration

Use direct Stripe when:

1. Shopify Payments Unavailable

If your business is in a country without Shopify Payments:

• Use Stripe as your primary processor
• Accept the additional Shopify transaction fees
• Or consider Shopify Plus (negotiated rates)

2. Advanced Fraud Protection (Stripe Radar)

Stripe Radar offers:

• Machine learning fraud detection
• Custom fraud rules
• 3D Secure optimization
• Block lists and allow lists

Radar features:
├── Default protection: Included with Stripe
├── Radar for Fraud Teams: $0.07/transaction
│   ├── Custom rules engine
│   ├── Manual review queues
│   └── Advanced analytics
└── Best for: High-risk merchants, large volumes

3. Stripe Billing (Subscriptions)

If you need subscription features beyond Shopify’s native capabilities:

• Metered billing
• Usage-based pricing
• Complex proration
• Dunning management

4. Stripe Connect (Marketplaces)

For multi-vendor marketplaces:

• Split payments between sellers
• Onboard sellers with Stripe accounts
• Handle marketplace payouts
• Manage platform fees

5. Unified Payment Data

If you have multiple properties:

• Single Stripe dashboard for all payments
• Consolidated reporting
• Unified customer records
• Cross-platform analytics

Fee Comparison

Shopify Payments (Recommended)

Direct Stripe + Shopify Fees

Example on $100 sale:

• Shopify Payments (Basic): $3.20 total fees
• Stripe Direct (Basic): $5.20 total fees
• Difference: $2.00 more per transaction

Setting Up Direct Stripe Integration

If you’ve determined direct Stripe is necessary:

Step 1: Create Stripe Account

1. Go to stripe.com
2. Sign up with business details
3. Complete identity verification
4. Activate your account

Step 2: Add Stripe to Shopify

1. Go to Settings > Payments
2. Scroll to Third-party payment providers
3. Click Choose third-party provider
4. Select Stripe
5. Connect your Stripe account

Step 3: Configure Payment Settings

In Shopify:

• Enable test mode first
• Configure capture settings (automatic/manual)
• Set up payment notifications

In Stripe Dashboard:

• Configure Radar rules
• Set up webhooks
• Enable relevant payment methods

Step 4: Test Transactions

1. Use Stripe test cards
2. Process test purchase
3. Verify order appears in both dashboards
4. Test refund workflow
5. Go live

Optimizing Stripe Performance

Enable Additional Payment Methods

Through Stripe, enable:

• Apple Pay / Google Pay (via Stripe)
• Buy now, pay later (Klarna, Affirm)
• Local payment methods (iDEAL, SEPA, etc.)
• Cryptocurrency (via Stripe integration)

Configure Stripe Radar

Recommended Radar rules:
├── Block high-risk countries (if applicable)
├── Require CVC for all cards
├── Block after 3 failed attempts
├── Review orders > $500 from new customers
└── Allow repeat customers with good history

Webhook Configuration

Set up webhooks for:

• payment_intent.succeeded
• payment_intent.payment_failed
• charge.refunded
• charge.dispute.created

Stripe Features Worth Considering

Stripe Sigma

SQL-based reporting for advanced analytics:

• Custom payment reports
• Revenue analytics
• Cohort analysis
• Export to data warehouse

Stripe Tax

Automatic sales tax calculation:

• 130+ countries supported
• Automatic rate determination
• Tax reporting
• Registration thresholds

Stripe Identity

Identity verification:

• Document verification
• Biometric matching
• Fraud prevention
• Age verification

Migrating Between Options

From Direct Stripe to Shopify Payments

1. Activate Shopify Payments
2. Complete verification
3. Set as primary payment method
4. Disable direct Stripe integration
5. Keep Stripe account for historical data

From Shopify Payments to Direct Stripe

1. Set up Stripe account
2. Add as payment provider
3. Disable Shopify Payments
4. Accept increased transaction fees
5. Gain access to full Stripe features

Cost-Benefit Analysis

When Direct Stripe Makes Financial Sense

Calculate the breakeven:

Monthly Stripe feature value needed to justify fees:

At $10,000 monthly revenue:
- Shopify Basic + Stripe: Extra $200/month in fees
- Need: $200+ value from Stripe features

At $100,000 monthly revenue:
- Shopify Basic + Stripe: Extra $2,000/month
- Need: $2,000+ value from Stripe features

Usually only justified for:
- High fraud reduction needs
- Marketplace/platform models
- Multi-property businesses
- Specific Stripe feature requirements

Recommendation Matrix

Troubleshooting

Issue: Stripe Payments Failing

Possible causes:

• Account not fully activated
• Webhook configuration issues
• API version mismatch

Solutions:

1. Check Stripe dashboard for errors
2. Verify webhook endpoints
3. Ensure API keys are correct
4. Test with Stripe test cards

Issue: High Decline Rates

Possible causes:

• Radar rules too strict
• 3D Secure issues
• Card brand restrictions

Solutions:

1. Review Radar rule performance
2. Optimize 3D Secure settings
3. Check blocked countries/cards
4. Analyze decline reason codes

Issue: Payout Delays

Possible causes:

• Account review in progress
• Reserve requirements
• Identity verification pending

Solutions:

1. Complete all verifications
2. Respond to information requests
3. Build transaction history
4. Contact Stripe support

Best Practices

Security

• Enable 3D Secure for high-risk transactions
• Keep API keys secure
• Monitor for suspicious activity
• Regularly review Radar rules

Performance

• Enable payment method caching
• Optimize checkout flow
• Minimize redirects
• Use Stripe Elements for best UX

Compliance

• Ensure PCI compliance
• Follow Stripe’s terms of service
• Handle disputes promptly
• Maintain proper documentation

2025 Snapshot

Quick benchmarks for the Stripe workflow. Use these as planning ranges, then validate against your own data.

Next Steps

After configuring your payment setup:

1. Test thoroughly - Process test transactions in all scenarios
2. Monitor performance - Track authorization and decline rates
3. Optimize fraud rules - Balance security and conversion
4. Consider alternatives - PayPal, Shop Pay for checkout options
5. Review regularly - Check fees and features annually

# List the 5 most recent orders (GraphQL)
curl -X POST "https://your-store.myshopify.com/admin/api/2025-01/graphql.json" \
  -H "X-Shopify-Access-Token: $SHOPIFY_ADMIN_TOKEN" \
  -H "Content-Type: application/json" \
  -d "{\"query\":\"{ orders(first: 5, sortKey: CREATED_AT, reverse: true) { edges { node { id name createdAt totalPriceSet { shopMoney { amount currencyCode } } customer { email } } } } }\"}"

Sources

• Stripe on Shopify App Store
• Shopify Payments overview
• Shopify: Online payments guide