Shopify vs. Stripe: A Comprehensive Comparison for Shopify Merchants
For Shopify merchants, selecting a payment gateway is one of the most critical operational decisions. It directly impacts your profit margins, your daily workflow, and your customer’s checkout experience.
The two most prominent options available are Shopify Payments and Stripe.
While they share the same underlying technology, they operate with different fee structures, policies, and dashboard integrations. This guide provides a detailed, informational comparison to help you determine which gateway aligns best with your business model.
Quick Comparison
| Feature/Aspect | Shopify Payments (Recommended) | Stripe (Standalone Account) |
|---|---|---|
| Best For | 95% of Merchants (Standard Retail) | High-Risk Industries or Unsupported Regions |
| Transaction Fees | 2.4% – 2.9% + 30¢ (Depends on Plan) | 2.9% + 30¢ (Standard Rate) |
| Extra “Shopify Tax” | $0 (Waived) | 0.5% – 2% (Third-Party Transaction Fee) |
| Total Cost ($100 Order) | $3.20 | $5.20 (approx. 60% higher fees) |
| “Killer” Feature | Shop Pay (Boosts conversion significantly) | Complete independence from Shopify’s policies |
| Dashboard Integration | Unified (Manage everything inside Shopify Admin) | Separate (Must log in to Stripe.com to view payouts) |
| Setup Difficulty | Easy (Pre-installed and ready to go) | Hard (Often hidden in settings for supported countries) |
| Payout Speed | 2-4 Business Days (Varies by country) | Rolling 2-7 Days |
| Global Availability | Limited (~23 Countries) | Extensive (46+ Countries) |
| Fraud Protection | Basic Fraud Analysis included | Advanced (Stripe Radar available) |
The Technical Relationship
Before comparing features, it is important to understand how these two services are related.
Shopify Payments is built on Stripe.
Technically, Shopify Payments is a white-label version of Stripe. Shopify uses Stripe’s infrastructure to process transactions but wraps it in its own interface. This means the reliability and security (PCI compliance) are identical between the two.
The Key Difference:
- Shopify Payments: You deal directly with Shopify. The gateway is fully integrated into your store admin.
- Stripe (Standalone): You deal with Stripe as a third-party entity. You have a separate account and dashboard independent of your Shopify store.
Shopify Payments vs. Stripe: Detailed Comparison
We will analyze the differences across four key dimensions: Pricing, Accepted Payment Methods, Ease of Use, and Payout Schedules.
1. Pricing Structure and Fees
Cost is usually the deciding factor for merchants. It is not just about the credit card processing rate; you must also consider the Third-Party Transaction Fee that Shopify charges when you do not use their native gateway.
Shopify Payments Fees
Shopify Payments does not charge a third-party transaction fee. Your rate depends on your Shopify subscription plan.
| Shopify Plan | Online Credit Card Rates | In-Person (POS) Rates | Third-Party Transaction Fee |
| Basic | 2.9% + 30¢ USD | 2.7% + 0¢ USD | 0% |
| Shopify | 2.6% + 30¢ USD | 2.5% + 0¢ USD | 0% |
| Advanced | 2.4% + 30¢ USD | 2.4% + 0¢ USD | 0% |
Stripe (Standalone) Fees
If you connect a personal Stripe account to Shopify, you pay Stripe’s processing fee PLUS Shopify’s third-party transaction fee.
- Stripe Standard Rate: 2.9% + 30¢ per transaction.
- Shopify Third-Party Fee: This varies by plan (2% for Basic, 1% for Shopify, 0.5% for Advanced).
2. Accepted Payment Methods
Both gateways support major credit cards, but Shopify Payments offers deeper integration with local payment methods and accelerated checkouts.
Shopify Payments Supports:
- Credit Cards: Visa, Mastercard, American Express, Discover, JCB, Diners Club.
- Digital Wallets: Apple Pay, Google Pay.
- Shop Pay: Shopify’s native accelerated checkout (allows customers to save shipping/billing info for faster purchases). Note: Shop Pay is exclusive to Shopify Payments.
- Local Payment Methods: Bancontact, iDEAL, EPS, Sofort (availability depends on the merchant’s region).
Stripe Supports:
- Credit Cards: Visa, Mastercard, American Express, Discover, JCB, Diners Club.
- Digital Wallets: Apple Pay, Google Pay, Alipay, WeChat Pay.
- Note: While Stripe supports many local methods technically, integrating them seamlessly into the Shopify checkout often requires additional configuration or third-party apps, whereas Shopify Payments has them built-in.
3. Ease of Use and UI
Shopify Payments:
- Setup: Activated directly within the Shopify Settings > Payments tab. Requires EIN/SSN and bank details.
- Dashboard: Unified. You can view payouts, chargebacks, and orders all within the Shopify Admin.
- Dispute Management: Chargebacks are handled directly inside the Shopify dashboard.
Stripe:
- Setup: Requires creating a separate account at Stripe.com and linking API keys (if applicable) or logging in via Shopify.
- Dashboard: Separate. You must log in to Stripe to view net payouts, detailed decline reasons, or export financial reports.
- Dispute Management: You must handle chargebacks and fraud alerts within the Stripe dashboard, not Shopify.
4. Payout Schedule
- Shopify Payments: Payout speeds vary by country.
- USA: 2 business days.
- UK/Australia: 2–4 business days.
- Japan: Weekly (Fridays).
- Stripe: Typically operates on a rolling schedule.
- USA: Rolling 2-day schedule.
- High Risk/New Accounts: May have a 7-day or 14-day rolling schedule initially.
Best Practices for Shopify Merchants
Based on the fee structures and integration capabilities, here are the recommended approaches for different merchant situations.
Situation A: Standard Retail Merchants
Recommendation: Use Shopify Payments.
For 95% of merchants selling standard physical goods, Shopify Payments is the logical choice.
- Reason 1: It is significantly cheaper because you avoid the 0.5%–2% third-party transaction fee.
- Reason 2: You gain access to Shop Pay, which can increase checkout conversion rates by streamlining the payment process for returning customers.
- Reason 3: Multicurrency support (Shopify Markets) is native, allowing you to sell in different currencies with automatic conversion.
Situation B: Merchants in Unsupported Regions
Recommendation: Use Stripe (if available).
Shopify Payments is not available in every country. If you are operating from a region where Shopify Payments is not supported, but Stripe is, Stripe becomes a top-tier alternative.
Situation C: Restricted Industries
Recommendation: Use Stripe (or a High-Risk Processor).
Shopify Payments has a strict Acceptable Use Policy (AUP). If you sell products that are considered “high risk” (e.g., adult products, vaporizers), Shopify Payments may reject your account.
Stripe generally has a slightly broader acceptance policy for certain business categories, though they also have restrictions. In these specific cases, using an external gateway is mandatory to avoid account suspension.
Frequently Asked Questions
Q: Can I use Stripe inside Shopify if I live in the US?
A: Generally, no. If Shopify Payments is available in your country, Shopify typically hides the option to add a standalone Stripe account. They prioritize their own gateway. You would only see Stripe as an option if you are in a country where Shopify Payments is not supported.
Q: Does using Stripe affect my checkout design?
A: No. The customer experience looks largely the same on the credit card entry field. However, you lose the “Shop Pay” branding and functionality, which is a distinct purple button that many customers recognize.
Q: What happens if I get a chargeback?
A:
- With Shopify Payments: You receive a notification in your Shopify Admin. You submit evidence (tracking numbers, policies) directly through Shopify. Cost: $15 USD (refunded if you win).
- With Stripe: You receive an email from Stripe. You must log into the Stripe dashboard to submit evidence. Cost: $15 USD (refunded if you win).
Q: Is Shopify Payments safer than Stripe?
A: They offer the same level of security. Both are PCI DSS compliant and use 3D Secure for fraud protection. The “safety” difference lies in policy: Shopify Payments is more sensitive to dropshipping shipping times and disputes, whereas Stripe focuses primarily on fraud rates and chargeback ratios.
Q: How do I actually enable Stripe in my Shopify admin?
A: Go to Settings > Payments in your Shopify admin.
Click “Choose a provider” (or “See all other providers”) in the “Payment providers” section.
Search for “Stripe” in the search bar.
Select it, and you will be redirected to log in and connect your Stripe account.
