Shopify Fees Explained: What You Really Pay Per Order

Shopify's fees are easy to underestimate because they arrive in pieces — a monthly charge here, a percentage there, a few cents per transaction. Added up across a month of orders, they're a real line in your profit math. Here's the full picture.

1. Subscription fee

Your monthly plan (Basic, Shopify, or Advanced). This is a fixed overhead cost — spread it across your orders to see its true per-order impact. At lower volumes it can be a surprisingly large slice of each sale.

2. Payment processing fees

The big one. Shopify Payments charges a percentage plus a flat fee per transaction (rates vary by plan and country — commonly around 2.4%–2.9% + ~30¢). On a $50 order that's roughly $1.50–$1.75 gone before you've counted product cost. Across hundreds of orders a month, processing fees are often a merchant's second- or third-largest cost after COGS and ads.

3. Third-party transaction fees

If you use an external payment gateway instead of Shopify Payments, Shopify adds an extra transaction fee (often 0.5%–2% depending on plan) on top of what your gateway charges. Using Shopify Payments avoids this surcharge — one of the few fee levers fully in your control.

4. Currency conversion & cross-border fees

Selling internationally? Currency conversion and cross-border fees apply on top of standard processing. Easy to forget, and they erode margin on exactly the orders that already cost more to ship.

5. App subscriptions

Every paid app in your stack is overhead. Individually small; collectively they can rival your Shopify subscription. Worth auditing quarterly.

What this means for your profit per order

Put together, a typical $50 order might look like this:

Line	Amount
Order revenue	$50.00
− Payment processing (2.9% + 30¢)	−$1.75
− Subscription (allocated)	−$0.40
− App costs (allocated)	−$0.30
Revenue after Shopify fees	$47.55

That's before COGS, shipping, refunds, and ad spend. Shopify fees alone took ~5% of the order. The platform reports the $50; the $47.55 is what you actually had to work with.

Fees don't feel big per order. They feel big at the end of the month — which is exactly when most merchants notice the gap.

How to see your real fees automatically

You don't have to estimate. ProfitPeek reads the actual payment fees from each Shopify transaction — not a flat percentage guess — and subtracts them, alongside COGS, refunds, shipping, and ad spend, to show your true net profit per day, product, and order.

Related: Shopify shows revenue, not profit · How to calculate COGS