What fees does Shopify charge per sale?

Payment processing (Shopify Payments is typically ~2.9% + $0.30 per order in the US) plus an extra transaction fee — usually 0.5%-2% depending on plan — if you don't use Shopify Payments.

Why is my Shopify store not profitable?

The most common reason is overhead the per-order math ignored: subscription, apps, theme, gateway penalty, and processing fees. Re-run profit monthly across all costs, not per order.

How much do Shopify apps cost per month?

Most stores run 3-7 paid apps in the $10-$40/month range. Five typical apps add up to $100-$200/month, which can swallow the entire profit of a small store.

Does Shopify charge extra for PayPal?

Yes if you're on lower-tier plans — Shopify adds an extra transaction fee on every order processed outside Shopify Payments, on top of PayPal's own cut. Higher-tier plans reduce the penalty but don't always eliminate it.

Why Your Shopify "Profit" Is Wrong (Fees & Apps You Forgot)

Unlike a marketplace that deducts everything before paying you, Shopify makes you the one responsible for subtracting your own costs — and most sellers' 'profit' only subtracts product cost. The real cost stack also includes payment processing, your monthly subscription, every paid app, your theme, and an extra transaction fee if you don't use Shopify Payments.

The short answer

Shopify doesn't deduct your overhead for you — you do. Most 'profit' math subtracts product cost and stops there, ignoring payment processing on every order, your monthly subscription, every paid app, your theme, and the extra transaction fee Shopify adds if you use a third-party gateway. Profit that ignores these can look healthy while the store quietly loses money.

1. Payment processing on every order

Shopify Payments (or any gateway) takes a percentage plus a flat fee per transaction on every single order. The flat component punishes low-order-value stores the same way it does on marketplaces.

2. The third-party gateway penalty

If you use an external payment provider instead of Shopify Payments, Shopify adds an extra transaction fee on top of what your gateway charges. The penalty is lower on higher-tier plans but never zero on the lower ones. Using PayPal-only on a Basic plan can mean paying two cuts.

3. The app subscription stack

Reviews app, email app, upsell app, shipping app, subscription-billing app — each is a recurring monthly charge. Five apps at $15-$40 each is easily $150+/month that never appears in per-order math but absolutely is overhead.

4. The base subscription and theme

Your monthly Shopify plan and any premium theme or one-time purchases are fixed overhead that must be spread across your order volume.

Worked example: per-order vs true profit

A store doing 200 orders/month at $45 average order and $18 product cost.

Per-order view: $45 minus $18 equals $27/order, times 200 equals $5,400 'profit.'

True monthly view: $5,400 gross profit minus $321 payment processing (~2.9% + $0.30 × 200) minus $39 subscription minus $150 apps equals $4,890 true profit.

A $510/month gap — over $6,000/year — that the per-order view hides entirely, and it gets worse at lower order values where the flat fees bite harder.

How to find your real Shopify profit

Pull payment processing totals from Shopify Payments payouts (not your gross sales). List every recurring app and subscription — most stores underestimate this by half. Check for the third-party gateway fee if you're not on Shopify Payments. Compute profit monthly across all overhead, then divide by orders for a true per-order figure.

Frequently asked questions

What fees does Shopify charge per sale?: Payment processing (Shopify Payments is typically ~2.9% + $0.30 per order in the US) plus an extra transaction fee — usually 0.5%-2% depending on plan — if you don't use Shopify Payments.
Why is my Shopify store not profitable?: The most common reason is overhead the per-order math ignored: subscription, apps, theme, gateway penalty, and processing fees. Re-run profit monthly across all costs, not per order.
How much do Shopify apps cost per month?: Most stores run 3-7 paid apps in the $10-$40/month range. Five typical apps add up to $100-$200/month, which can swallow the entire profit of a small store.
Does Shopify charge extra for PayPal?: Yes if you're on lower-tier plans — Shopify adds an extra transaction fee on every order processed outside Shopify Payments, on top of PayPal's own cut. Higher-tier plans reduce the penalty but don't always eliminate it.

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