Shopify makes pricing look simple: pick a plan, pay a percentage, start selling. But when store owners actually sit down and ask "how much am I paying in fees every month?", almost nobody can answer. That is because Shopify fees hide in three separate layers that stack on top of each other.
The 3 Layers of Shopify Fees
Layer 1 — Subscription. The flat monthly price of your plan (roughly $39 for Basic, $105 for Shopify, $399 for Advanced). Easy to see, easy to forget in margin math.
Layer 2 — Credit card rate. If you use Shopify Payments, every online order is charged a percentage plus a fixed fee. Typical online rates are around 2.9% + $0.30 on Basic, 2.6% + $0.10 on Shopify, and 2.4% + $0.10 on Advanced.
Layer 3 — Third-party gateway fee. If you do NOT use Shopify Payments and connect your own payment provider, Shopify adds an extra transaction fee on top: roughly 2% on Basic, 1% on Shopify, and 0.5% on Advanced. This is the layer that silently destroys margins.
The Formula
Total monthly fees = Subscription
+ (Revenue × Card rate)
+ ($0.30 × Number of orders)
+ (Revenue × Gateway fee, if not on Shopify Payments)
Worked Example
Imagine a store doing $10,000/month across 200 orders on the Basic plan, using Shopify Payments:
- Card percentage: $10,000 × 2.9% = $290
- Fixed fees: 200 orders × $0.30 = $60
- Subscription: $39
- Total: $389/month (about 3.9% of revenue)
Now the same store using a third-party gateway instead of Shopify Payments adds 2% of revenue: +$200. Total jumps to $589/month — nearly 6% of revenue gone before product costs, shipping, or ads.
3 Ways to Pay Less
- Use Shopify Payments if available in your country. It removes Layer 3 entirely.
- Run the plan-upgrade math. If you process $50,000/month, moving from Basic (2.9%) to Shopify (2.6%) saves about $150/month — more than the $66 plan price difference.
- Raise your AOV. The $0.30 fixed fee hurts on $15 orders and barely matters on $80 orders. Bundles and upsells directly reduce fee percentage.
Stop estimating. Calculate it exactly.
Enter your revenue, orders, and plan — get your true net profit after every fee.
Open Shopify Profit Calculator →Fees are only one ingredient in your margin. Pair this with our E-commerce Profit Calculator and Profit Margin Calculator to see the full picture before you price your next product.