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Shopify charges two types of fees on every sale: a payment processing fee (similar to Stripe's rate) and a separate transaction fee if you use a third-party payment gateway instead of Shopify Payments. Understanding both is essential for accurate margin calculation.
Shopify fee structure by plan
| Plan | Monthly fee | Processing rate | Transaction fee (3rd party) |
|---|---|---|---|
| Basic | $39 | 2.9% + $0.30 | 2.0% |
| Shopify | $105 | 2.6% + $0.30 | 1.0% |
| Advanced | $399 | 2.4% + $0.30 | 0.5% |
The transaction fee applies only when you use a payment processor other than Shopify Payments (Stripe, PayPal, etc.). Using Shopify Payments eliminates this fee entirely.
Shopify Payments vs third-party gateways
For most merchants, Shopify Payments is the cheapest option because it eliminates the transaction fee. A $100 sale on the Basic plan via Stripe costs $2.90 + $0.30 + $2.00 = $5.20, compared to just $3.20 with Shopify Payments — a 62% difference.
Reasons to use a third-party gateway anyway: - Your country isn't supported by Shopify Payments (Shopify Payments is available in 17+ countries) - You need specific fraud tools, subscriptions, or features only available in your existing gateway - High-risk product categories that Shopify Payments doesn't support
Frequently asked questions
Does the monthly plan fee factor into per-sale cost? The calculator shows per-transaction fees only. For a full cost-per-sale picture including the plan fee, divide your monthly plan fee by your number of monthly transactions and add it to the per-transaction total. At 100 sales/month on the Basic plan, the plan overhead is $0.39/sale.
Should I upgrade my plan to get lower fees? The upgrade math: if moving from Basic to Shopify ($66/month more) saves 0.3% + eliminates 1% transaction fee (if on 3rd-party): on $66/$0.013 = $5,077/month in sales you break even. Above that volume, upgrading pays off.