Shopify Payments Fees Compared to Stripe: A Detailed Guide

Introduction

Choosing between Shopify Payments and Stripe involves more than comparing two percentage rates. While both processors share a technical foundation, the way they impact your monthly margins depends on your Shopify plan and where your customers live. A single percentage point difference can result in thousands of dollars in lost revenue as your store scales.

We built HidePay — free to install to give merchants control over these variables at checkout. Many store owners find that certain payment methods are too expensive in specific regions or for specific products. This guide breaks down the fee structures of both Shopify Payments and Stripe to help you choose the most cost-effective path for your business.

We will cover domestic and international transaction rates, the impact of Shopify’s third-party transaction fees, and how hidden costs like chargebacks and currency conversions influence your bottom line. This analysis provides the practical data you need to optimize your checkout for maximum profitability. For a short product overview, see our announcement post introducing HidePay for Shopify.

The Core Fee Structures Compared

The most visible cost of any payment processor is the transaction fee. Both Stripe and Shopify Payments use a "cents plus percentage" model. However, the flat percentage you pay varies based on your Shopify subscription level.

Shopify Payments Domestic Rates

Shopify Payments offers tiered pricing. As you move to higher Shopify plans, your transaction fees decrease. For domestic credit card transactions in the United States, the rates typically follow this structure:

• Basic Plan: 2.9% + 30¢ USD
• Shopify Plan: 2.6% + 30¢ USD
• Advanced Plan: 2.4% + 30¢ USD

These rates apply to "Online" transactions, also known as Card-Not-Present (CNP). If you use Shopify POS for in-person sales, the rates are lower, ranging from 2.4% to 2.7% with no additional cents-per-transaction fee in some regions.

Stripe Domestic Rates

Stripe generally maintains a flat pricing model for most merchants. For domestic card payments in the United States, the standard rate is 2.9% + 30¢ per successful transaction. Unlike Shopify Payments, Stripe does not offer lower rates simply because you pay for a higher software subscription elsewhere.

For high-volume merchants, Stripe offers custom "Interchange Plus" (IC+) pricing. This model is usually reserved for businesses processing over $100,000 per month. IC+ pricing separates the card network fees from Stripe's markup, which can lead to significant savings for businesses with large average order values.

The Third-Party Transaction Fee Penalty

The most critical factor for Shopify merchants is the third-party transaction fee. If you choose to use Stripe as your primary gateway instead of Shopify Payments, Shopify charges an additional fee on every transaction.

Shopify applies this fee because they prefer merchants to stay within their native ecosystem. The cost of this "penalty" depends on your plan:

• Basic Plan: 2.0% additional fee
• Shopify Plan: 1.0% additional fee
• Advanced Plan: 0.5% additional fee

If you are on the Basic plan and use Stripe, your total cost for a domestic transaction would be 4.9% + 30¢ (2.9% from Stripe + 2.0% from Shopify). This makes Stripe significantly more expensive for the vast majority of Shopify users. To make Stripe cost-effective, you typically need to be on the Shopify Plus or Advanced plans where the additional fee is lower, or have a custom IC+ deal with Stripe that offsets the 0.5% penalty.

International Transaction Fees and Currency Conversion

Selling globally introduces two additional layers of cost: international card processing fees and currency conversion fees. Both processors handle these differently.

Cross-Border Fees

When a customer uses a card issued outside your home country, processors charge an extra fee to cover the increased risk and communication between international banks.

• Shopify Payments: Usually charges an additional 1% for international cards. In some regions, like the UK or EU, these fees vary based on whether the card is "non-EEA" (European Economic Area).
• Stripe: Also charges an additional 1.5% for international cards. If currency conversion is required, Stripe adds another 1% fee.

Currency Conversion

If you sell in multiple currencies, you must account for the mid-market rate and the processor's markup.

Shopify Payments charges a currency conversion fee when it converts your customer's local currency into your payout currency. In the United States, this fee is typically 1.5%. In other countries, it can be as high as 2.0%.

Stripe handles currency conversion similarly, typically adding 1% to 2% to the mid-market exchange rate. However, Stripe provides more flexibility for merchants with international bank accounts. If you have a bank account in the currency you are selling in, Stripe can often pay you out in that currency without an exchange fee. Shopify Payments is more restrictive regarding payout currencies and bank account locations.

Hidden Costs: Chargebacks, Refunds, and Subscriptions

The headline transaction rate is only one part of the financial picture. Operational events like disputes and refunds carry their own costs.

Chargeback Fees

A chargeback occurs when a customer disputes a transaction through their bank. Both processors charge a fee for the administrative work of managing the dispute.

• Shopify Payments: Charges a flat $15 fee (in the US) per dispute. If you win the dispute, Shopify refunds this $15 fee to you.
• Stripe: Also charges a $15 fee per dispute. However, unlike Shopify, Stripe does not refund this fee if you win the case.

Refund Policy

When you refund a customer, neither Shopify Payments nor Stripe returns the original transaction fees. If a customer buys a $100 item and you pay $3.20 in fees, you are out that $3.20 even if you return the full $100 to the customer. This makes "Change of Mind" returns a direct expense for your business.

Subscription Billing

If your store uses a subscription model, Stripe has a distinct advantage. Stripe Billing is a highly advanced tool for managing recurring payments. However, Stripe charges an additional 0.4% to 0.7% for recurring transactions.

Shopify Payments supports subscriptions through third-party apps. While you don't pay a specific "subscription fee" to Shopify for the payment processing, you will likely pay a monthly fee or a percentage of sales to the subscription app you choose (like Recharge or Bold).

Why Checkout Customization Matters for Fee Management

Choosing a processor is the first step, but managing which payment methods appear to which customers is how you protect your margins. Not all payment methods are created equal. Some carry higher fraud risks, while others have significantly higher fees (like Buy Now, Pay Later options).

HidePay allows you to create a payment customization that shows or hides payment methods based on specific conditions. For example, if you know that international credit card fees are eating your profits on low-margin items, you can create a rule to hide certain credit card options for international orders and promote lower-fee alternatives.

Using our tool, you can also:

• Sort and rename payment methods: Move lower-fee options like bank transfers or domestic cards to the top of the list.
• Rename methods: Label payment options clearly to reduce customer confusion and support requests.
• Hide payment methods by cart total or other conditions: If a transaction is too small to justify the 30¢ flat fee, you can limit which methods are available.

If you need to hide Express Checkout buttons (PayPal/other accelerated options), see the guide on how to hide Express Checkout with HidePay.

By being intentional about your checkout configuration, you reduce the friction that leads to cart abandonment and lower your overall processing costs. We designed HidePay to make this process straightforward for merchants who want to move beyond "one size fits all" payments. If you also need to manage shipping methods to avoid margin-eating delivery choices, consider pairing HidePay with HideShip on the Shopify App Store or learn more about the combined offering in our HideSuite bundle announcement.

Payout Schedules and Cash Flow

The speed at which you receive your money impacts your ability to restock inventory and pay for marketing.

• Shopify Payments: Offers a predictable payout schedule. In the US, payouts typically take 2 business days. You can track exactly which orders are included in each payout directly from your Shopify admin. This deep integration makes reconciliation much faster for your bookkeeper.
• Stripe: Also offers a 2-day rolling payout in the US. However, your first payout often takes 7 to 14 days while Stripe performs initial risk verification. Stripe's dashboard is separate from Shopify, which means you will spend more time matching bank deposits to Shopify orders unless you use an automation tool.

Technical Foundation: Shopify Functions

It is important to note that the way payment methods are managed in Shopify has changed. Previously, merchants had to use Shopify Scripts, which were only available to Shopify Plus users and often caused performance issues.

HidePay is built on native Shopify Functions. This technology allows the app to run directly within Shopify's core infrastructure. For you, this means the app is faster, more reliable, and does not require theme code edits. Because it is native, it works correctly with Shopify's "Built for Shopify" standards, ensuring it won't break during high-traffic events like Black Friday. For background on why functions replaced scripts, read our post on Why Shopify Functions are the future.

When to Choose Shopify Payments

For most merchants, Shopify Payments is the clear winner for three reasons:

1. No Extra Fees: You avoid the 0.5% to 2% third-party transaction penalty.
2. Integrated Experience: Your payouts, disputes, and financial reporting are all in one place.
3. Shop Pay: You gain access to Shop Pay, which is one of the highest-converting accelerated checkouts available.

If you are a merchant based in a supported country (like the US, Canada, UK, or Australia) and you are not selling prohibited items, Shopify Payments should be your default choice.

When to Choose Stripe

Despite the extra fees, Stripe is a better choice for specific types of businesses:

• Unsupported Countries: If your business is registered in a country where Shopify Payments is not available, Stripe is often the most reliable alternative.
• Complex Business Models: If you run a marketplace where you need to split payments between multiple vendors (Stripe Connect), Stripe's API is far more capable.
• Custom Checkouts: If you use a "headless" setup or a custom-built checkout outside of the standard Shopify framework, Stripe provides the flexibility you need.
• High-Risk Categories: Some industries are prohibited by Shopify Payments' terms of service but may be accepted by Stripe's specialized high-risk underwriting.

Strategic Decision Framework

To decide which processor fits your needs, evaluate your business against these four criteria:

1. Your Shopify Plan

If you are on the Basic or Shopify plan, the 1.0% to 2.0% third-party fee makes Stripe almost impossible to justify. On these plans, the combined fees would likely exceed 4% of every sale. Only Advanced or Plus merchants should seriously consider Stripe for domestic sales.

2. Average Order Value (AOV)

The 30¢ flat fee impacts low-AOV stores more heavily. If you sell $5 items, that 30¢ represents 6% of your revenue. In this case, you should prioritize the processor that offers the lowest flat fee. Shopify Payments sometimes offers "Micropayment" rates in specific regions, which can be a deciding factor.

3. International Sales Volume

If more than 30% of your sales come from abroad, look closely at the FX (Foreign Exchange) markup. If you have a local bank account in your secondary market, Stripe might allow you to avoid conversion fees entirely, whereas Shopify Payments might force a 1.5% conversion.

4. Risk and Chargebacks

If you sell high-risk products (like high-end electronics or designer goods), your chargeback rate may be higher. Because Shopify Payments refunds the $15 dispute fee if you win, it can save you hundreds of dollars per year compared to Stripe.

How to Optimize Your Current Setup

Regardless of which processor you use, you are likely leaving money on the table by showing every payment method to every customer. Use the following steps to improve your margins:

• Review your payout reports: Identify which countries have the highest international fees.
• Identify high-fee methods: Check your "Buy Now, Pay Later" (BNPL) usage. These often cost 5% to 6% per transaction.
• Implement conditional rules: Use HidePay to hide BNPL options for small orders where the margin is thin (see the guide on hiding payment methods by cart currency for currency-specific rules).
• Promote domestic options: If you have a local payment method (like iDEAL in the Netherlands or Interac in Canada), ensure it is sorted to the top for those customers.

By being intentional about your checkout configuration, you reduce the friction that leads to cart abandonment and lower your overall processing costs. We designed HidePay to make this process straightforward for merchants who want to move beyond "one size fits all" payments.

Conclusion

Shopify Payments is the most cost-effective solution for the vast majority of Shopify merchants due to the integrated nature of the platform and the absence of third-party transaction fees. Stripe remains a powerful tool for global businesses with complex technical requirements or those operating in countries where Shopify's native processor is unavailable.

Key takeaways for your business:

• Avoid the penalty: Using Stripe on Shopify adds a 0.5%–2% fee on top of Stripe’s own rates.
• Watch international fees: Both processors add roughly 1%–1.5% for international cards.
• Protect your margins: Use rules to hide expensive or high-risk payment methods in specific scenarios.
• Leverage native tools: Use apps built on Shopify Functions for better performance and reliability.

Ready to take control of your checkout costs? Get HidePay for your store today to start sorting, renaming, and hiding payment methods based on your unique business needs. If you need installation steps, see the guide on how to install HidePay.

FAQ

Does Stripe or Shopify Payments have a monthly fee?

Neither Stripe nor Shopify Payments charges a standalone monthly fee for payment processing. Stripe is a pay-as-you-go service. Shopify Payments is included with your Shopify subscription, though you must pay for a Shopify plan (Basic, Shopify, or Advanced) to access the platform.

Will I be charged extra if I use Stripe on Shopify?

Yes. If you use a third-party gateway like Stripe instead of Shopify Payments, Shopify charges an additional transaction fee. This fee is 2% on the Basic plan, 1% on the Shopify plan, and 0.5% on the Advanced plan. This is in addition to the fees Stripe charges you.

Which processor is better for international selling?

Shopify Payments is generally easier for international selling because it integrates with Shopify Markets. However, Stripe can be more cost-effective if you have bank accounts in multiple countries. Stripe allows you to receive payouts in different currencies more flexibly, potentially avoiding some conversion fees.

What happens to the fees when I refund a customer?

Both Stripe and Shopify Payments keep the original transaction fees when you issue a refund. You will have to pay the customer back the full amount, but the processor will not return the percentage or the flat fee they collected during the initial sale.

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Further reading and resources:

• Product announcement: Introducing HidePay for Shopify (Nextools blog)
• Why Shopify Functions are the future (Nextools blog)
• HidePay docs: Sort and rename payment methods | How to create a payment customization | How to hide Express Checkout with HidePay | How to hide payment methods by cart currency
• Related apps: HideShip (manage shipping methods) | HideSuite (bundle) | CartBlock (order validation)