If your store runs on Basic and checks out through Stripe or PayPal, you are probably paying Shopify 2% of revenue for nothing. That fee is not a processing cost. It is the price of not using Shopify Payments, and on most US stores I would turn it off this week.
My opinion, plainly: for a typical US Shopify store, the fee stack is the cheapest margin win you will find. It comes before new creative, before a theme rebuild, before another app. Below is the whole stack with worked numbers, and the short list of cases where a third-party gateway still makes sense.
Want your own numbers first? The Shopify transaction fee calculator does the arithmetic for your plan, AOV and order count. This post explains what it is measuring.
The three fees people mix up
Most confusion comes from treating “Shopify fees” as one number. There are three:
- Card processing. A percentage plus a fixed amount per order, taken by whoever processes the card. With Shopify Payments that is Shopify. With Stripe, PayPal or Authorize.net it is them.
- Shopify’s third-party transaction fee. An extra percentage Shopify charges when an order is processed by anything other than Shopify Payments. It is added on top of the gateway’s own fee and does not replace it.
- The plan subscription. The monthly software fee. It is separate from per-order costs, but it changes both of the numbers above.
2026 US online rates, by plan
These are approximate US list rates for standard online cards. Check Shopify’s pricing page and your own bill before you budget on them.
| Plan | Shopify Payments (online) | Third-party surcharge |
|---|---|---|
| Basic | ~2.9% + $0.30 | 2.0% |
| Grow | ~2.7% + $0.30 | 1.0% |
| Advanced | ~2.5% + $0.30 | 0.6% |
| Plus | ~2.15–2.25% + $0.30 (negotiated) | ~0.2% |
Premium, Amex-style and international cards cost more on Shopify Payments, and in-person rates are lower. For most stores, though, domestic online cards are most of the volume, and that is what matters for this decision.
Worked example: a $102k/month store on Basic
Say a US store averages an $85 order and does 1,200 orders a month. That is $102,000 in card sales.
Basic with Shopify Payments (2.9% + $0.30):
- Percentage: $102,000 × 2.9% = $2,958
- Fixed: 1,200 × $0.30 = $360
- Total: about $3,318 a month (3.25% effective)
Basic with Stripe at 2.9% + $0.30, plus Shopify’s 2%:
- Stripe: $2,958 + $360 = $3,318
- Shopify third-party fee: $102,000 × 2% = $2,040
- Total: about $5,358 a month (5.25% effective)
Same orders, same customers, and the gateway choice alone costs $2,040 a month, or about $24,500 a year. If that store’s net margin is 10%, the gateway is eating a fifth of its profit.
Worked example: low AOV, high volume
Low-AOV stores get hit twice: once by the fixed $0.30 and again by the surcharge. Say a store sells $32 replenishment products and ships 4,000 orders a month ($128,000 GMV).
- Basic + Shopify Payments: $3,712 + $1,200 fixed = $4,912 (3.84% effective). Notice the thirty cents adds almost a full point.
- Basic + third-party: $4,912 + $2,560 surcharge = $7,472.
- Grow + Shopify Payments: $3,456 + $1,200 = $4,656, which saves about $256 a month on processing compared with Basic. That only pays off once the savings cover Grow’s higher subscription.
That is the trade the calculator is built for. A plan upgrade is a fee decision only once processing savings beat the subscription difference. Before that point you are buying it for the features.
When a third-party gateway is still the right call
I don’t tell every store to switch blindly. These are good reasons to keep a third-party path:
- Shopify Payments isn’t available for your country or business entity.
- You have payout, banking or currency requirements Shopify Payments can’t meet yet.
- A regional payment method that converts noticeably better is only available through a local PSP.
- You have a negotiated processor contract below Shopify’s rates. That is plausible at Plus volume and rare on Basic.
These are not good reasons: “the agency set up Stripe and nobody revisited it,” “we’ve always used PayPal,” and “we might need Authorize.net one day.”
One caveat: even with Shopify Payments as your main processor, some payment methods can still trigger third-party-style fees. Read the transaction fee section of your actual Shopify bill. The pricing page is not your invoice.
What I’d do
- Open last month’s Shopify bill and find the transaction fee line. If it isn’t zero and you’re in a Shopify Payments country, find out which payment method is causing it.
- Put your real AOV and order count into the fee calculator and flip only the Payments toggle. If the gap is more than a few hundred dollars a month, plan the switch. It’s usually a settings change, not a project.
- Model peak season, not an average month. Run the numbers at 2–3× your normal volume. That is when a surcharge stops being a rounding error, and when a plan upgrade starts paying for itself.
Next, look at PayPal specifically. It is the most common reason a store on Shopify Payments still pays the surcharge. I go through it in PayPal fees vs Shopify Payments.
Work with me
I’m Faraz, a Shopify and AI automation consultant. If you want a second pair of eyes on your fee stack, checkout setup or margins, I can audit the store and give you a short list of what to change, in order. Get in touch at farazhussain.com or WhatsApp +92 334 3454747.
Rates are approximate 2026 US list prices, used here for planning only. Confirm current rates in your Shopify admin before making decisions.