Shopify Payments costs between 1.6% and 3.2% per transaction plus a fixed fee of CHF 0.30 – depending on your Shopify plan and chosen payment method. For Swiss online shops, this is often cheaper than external payment providers, since no additional transaction fees apply.
Shopify Payments is the native payment gateway of the popular e-commerce platform. It processes credit cards, PayPal, and since 2025, also TWINT directly through your Shopify dashboard.
For Swiss merchants, these fees are particularly relevant because they make up a large portion of ongoing operating costs. A typical online shop pays between 2 and 4% of its revenue for payment processing.
The biggest cost factors are credit card fees, hidden currency conversion costs, and Swiss VAT of 7.7% on Shopify fees. With the right strategy, these costs can be significantly optimized.
What is Shopify Payments and why should you use it?
Shopify Payments is Shopify’s integrated payment system that processes credit cards, PayPal, TWINT, and other payment methods directly through your shop dashboard. Instead of using external providers like Stripe or Adyen, everything runs through a single interface.
The biggest advantage: You save the additional transaction fees that Shopify normally charges for external payment providers. These range from 0.5% to 2% per transaction depending on your plan.
Plus, your bookkeeping becomes significantly simpler. All payments, refunds, and chargebacks are seamlessly integrated into one system. This means less work reconciling different payment service providers.
The main advantages at a glance:
- No additional transaction fees with Shopify
- Automatic synchronization of all payment data
- Faster payouts (usually within 2-3 business days)
- Built-in fraud protection and chargeback management
- Optimized checkout including express function
Disadvantages include limited flexibility – Amazon Pay can’t be integrated, for example – and expensive chargebacks on returns.
Particularly important for Swiss shops: Since this year, Shopify Payments finally supports TWINT directly. This was long the main reason why many Swiss merchants had to rely on external providers.
The Complete Fee Overview for 2025
Credit Card Fees by Shopify Plan
Credit card fees with Shopify Payments vary between 2.55% and 3.2% per transaction plus CHF 0.30 fixed fee, depending on your plan. Higher plans offer better rates because Shopify assumes you’re generating more revenue.
| Plan | Swiss Cards | International Cards |
|---|---|---|
| Basic Plan | 2.95% + CHF 0.30 | 3.2% + CHF 0.30 |
| Grow Plan | 2.75% + CHF 0.30 | 2.9% + CHF 0.30 |
| Advanced Plan | 2.55% + CHF 0.30 | 2.7% + CHF 0.30 |
The distinction between domestic and international cards becomes particularly noticeable if you sell a lot abroad. A German card costs you 1.1-1.6% more than a Swiss card, for example.
The fixed fee of CHF 0.30 per transaction can add up with small order values. On a CHF 20 purchase, that’s already 1.5% – in addition to the percentage fee.
Visa and Mastercard are the two most widely accepted credit card networks in Switzerland. With Shopify Payments, you automatically support both, plus American Express and other international cards. Apple Pay and Google Pay payments are subject to the same transaction fees as credit card payments.
PayPal Fees
PayPal through Shopify works in two ways: as PayPal Express Checkout with your own PayPal rates or integrated through Shopify Payments with multi-currency support and unified fees.
With PayPal Express Checkout, customers see the PayPal button and process payment directly through PayPal. Normal PayPal fees vary depending on transaction type, potential currency conversion costs, PayPal account type, and individual agreements. They’re around 3.4% + CHF 0.55 per transaction.
With PayPal through Shopify Payments, transaction fees are identical to credit card fees. No separate PayPal fees apply.
The special feature: If you use Shopify Markets with Shopify Payments for multiple currencies, PayPal can accept orders in the respective customer currency. Refunds then also occur in the same currency – this saves exchange rate fees.
This is particularly handy if you sell to Germany and Austria simultaneously. PayPal processes Euro payments in Euros without having to convert everything to CHF.
Alternative Payment Methods and Their Costs
Besides credit cards and PayPal, Shopify Payments in Switzerland mainly supports TWINT and various buy-now-pay-later options. Fees vary considerably depending on the payment method.
TWINT has been directly integrated into Shopify Payments since June 2025 – a milestone for Swiss shops. You no longer need a separate TWINT account and save the annual plugin costs of about 120 francs. TWINT costs only about 1.6% per transaction through Shopify Payments, including the fixed CHF 0.30 fee.
This is significantly cheaper than previous solutions through Wallee or Mollie, which caused about 3% total fees. Especially for mobile purchases and small order values, TWINT is thus more attractive than credit cards.
For special requirements, Abilita can be an alternative. Abilita is a white-label payment service provider that supports many different payment methods and even assumes payment default risk. This can be interesting for larger shops that need individual terms.
TWINT is the most important local Swiss payment method. While Germany has Giropay and instant transfers, the Swiss market focuses heavily on credit cards, PayPal, and TWINT.
Hidden Costs You Should Know About
In addition to obvious transaction fees, Swiss shops also face VAT, currency conversion fees, and PayPal additional costs. These hidden costs can increase your actual payment fees by 50-100%.
Swiss VAT of 7.7% is charged on all Shopify Payments fees. So if you pay 2% credit card fees, you add 7.7% VAT on top – making it effectively 2.15% instead of 2%.
An even bigger cost factor is currency conversions. Shopify Payments usually charges 1.5-2% additional conversion fee if you want payouts in CHF but have revenues from EUR shops. The solution: Multi-currency setup with separate bank accounts in the EU and Switzerland.
PayPal is particularly expensive with currency conversions. First, the normal payment fee is deducted (3.4% + fixed amount), then an exchange rate fee of 2.5-4% if the currency doesn’t match your PayPal account currency.
The solution: Maintain PayPal accounts in multiple currencies and manually convert earnings at better rates. This often saves 1-2% per transaction.
Shopify Plus: Lower Fees for Larger Shops
Shopify Plus offers significantly lower payment fees and individually negotiable terms from about 1 million CHF annual revenue. The enterprise solution starts at CHF 2000 per month but often brings massive savings on transaction fees.
While normal Shopify plans have fees between 2.55 and 2.95% + 0.30 CHF, Shopify Plus only charges 2.3% + 0.30 CHF.
With six-figure annual revenues, you can easily save several thousand francs in transaction fees.
Besides reduced fees, Shopify Plus also offers extended B2B functions, better API limits, and priority support. For larger shops, it’s often the only alternative.
The rule of thumb: From 500,000 CHF annual revenue, it’s worth having a conversation about Shopify Plus. From 1 million CHF, it almost always becomes cheaper than normal plans.
How to Optimize Your Payment Costs
Shopify Payments is often cheaper than external providers because you save the additional transaction fees of 0.5-2%. An external provider like Stripe costs 1.4% + CHF 0.25, for example, but Shopify charges an additional 1% transaction fee – making it 2.4% total instead of 1.6% with TWINT through Shopify Payments.
Plan selection should be based on your monthly transaction volume. Rule of thumb: With more than CHF 10,000 monthly revenue, the next higher plan usually pays off due to lower transaction fees.
Annual payment saves about 16% of basic fees on all Shopify plans. That’s only a few hundred francs per year, but savings are savings.
Strategic combination of different payment providers can save additional costs. Example: TWINT through Shopify Payments (1.6%), credit cards through a specialized provider with better rates for international cards.
Typical mistakes Swiss shops make with Shopify project costs:
- No TWINT leads to lower mobile conversion. Integrate TWINT through your PSP and place it prominently in accelerated checkout. Mobile users in Switzerland expect TWINT as a payment option.
- Incorrect VAT settings after 2024 lead to wrong prices and tax reports. Update all tax rates and shipping tax codes and retest discounts.
- No QR bills for invoice workflows slows B2B payment processing. Add QR bills to PDFs and offer eBill for recurring business customers.
- Single-language shops miss half the market. Localize product content, customer service, and transaction emails in DE/FR/IT. Check out our post on the best translation apps for Shopify.
Conclusion
The main cost factors with Shopify Payments are plan-dependent credit card fees (2.3-3.2%), hidden currency conversion costs (1.5-2%), and Swiss VAT (7.7% on all fees).
For small to medium shops (up to 500,000 CHF annual revenue), one of the three standard Shopify plans is usually optimal. Larger shops should check out Shopify Plus.
For very large shops (over 2 million CHF annual revenue), Shopify Plus with negotiated terms becomes practically always cheaper. The fee savings finance the higher basic costs.
The integration of TWINT into Shopify Payments in 2025 was a milestone for Swiss shops. For the first time, all important payment methods can be processed natively through Shopify.
Our tip: Start with Shopify Payments and TWINT, monitor your actual costs including all hidden fees, and only optimize once you know the exact cost drivers.
If you have questions about the optimal payment strategy for your shop, we’re happy to help – as Shopify experts, we know the pitfalls and optimization opportunities from a variety of projects.