Three layers of cost on every sale
Ecommerce fees stack in three layers. First, the platform subscription you pay whether you sell or not. Second, a per-sale platform transaction fee on some plans. Third, the payment processor's fee, which every seller pays. On top of those sit event fees that only appear when something happens: a foreign card, a currency conversion, a dispute, or an instant payout.
All rates here are US standard rates from Shopify, Webflow, systeme.io, Stripe and PayPal pricing and help pages read on 30 October 2026. Rates differ by country and change over time, and negotiated or high-volume rates are not covered. This is a research guide, not a payments test.
The glossary
| Term | Plain definition | Where it appears (US, 30 Oct 2026) |
|---|---|---|
| Plan or subscription fee | The fixed monthly or yearly price of the store platform. | Shopify Basic $29/mo on yearly billing ($39 monthly); Webflow Ecommerce Standard $29/mo billed yearly; systeme.io Free $0, Startup $17/mo. |
| Processing fee | The processor's charge for handling a card payment, usually a percentage plus a fixed amount. | Stripe 2.9% + 30 cents; Shopify Payments on Basic 2.9% + 30 cents online; PayPal standard card payments 2.99% + $0.49. |
| Fixed fee | The flat part of the processing fee, charged per transaction regardless of size. | Stripe 30 cents; PayPal $0.49. It hits small orders hardest. |
| Platform transaction fee | A percentage the store platform takes on top of processing. | Webflow Ecommerce Standard 2%, Plus and Advanced 0%; systeme.io 0% on all plans. |
| Third-party transaction fee | Shopify's extra fee when you use a payment provider other than Shopify Payments. | Shopify Basic 2%, Grow 1%, Advanced 0.6%. |
| International card fee | A surcharge when the card was issued in another country. | Stripe +1.5%; PayPal +1.50% on international commercial transactions. |
| Currency conversion fee | A surcharge when the payment must be converted between currencies. | Stripe +1%; PayPal lists a 3.00% or 4.00% spread depending on the transaction. |
| Chargeback | The cardholder's bank reverses a payment and takes the money back while the dispute runs. | Shopify Payments: bank takes the amount and a fee right away. |
| Inquiry | The bank asks questions before deciding whether to charge back. | Shopify Payments: no money or fee taken yet. |
| Dispute or chargeback fee | The processor's charge for handling a dispute. | Stripe $15 per dispute; Shopify Payments US $15, returned if you win; PayPal $20 chargeback fee on card transactions, $15 dispute fee on PayPal-account transactions. |
| Dispute countered fee | A charge for responding to a dispute. | Stripe $15 if you respond manually, refunded if you win. |
| Refund cost | What you lose when you refund. | Stripe and PayPal do not return the original processing fees; issuing the refund itself is free. Webflow says there is no fee for issuing a refund. |
| Payout | The transfer of your sales money to your bank. | Stripe standard payouts are free; Webflow says PayPal funds land in your PayPal account and Stripe funds in your linked bank. |
| Instant payout fee | A charge for receiving money faster than the standard schedule. | Stripe 1.5% of the payout, minimum 50 cents. |
| Fee base | The amount a percentage is calculated on. | Webflow calculates its transaction fee on the order total including taxes. |
Worked example: one $50 sale, every fee line
Assume a US buyer pays $50 with a domestic card, no tax, no shipping, and the store makes 40 sales a month. The 40 sales figure is hypothetical; it is only there to spread the monthly plan fee across orders. Rates are each vendor's published US standard rate.
- Foreign card on Stripe: add 1.5%, or $0.75 on this sale.
- Currency conversion on Stripe: add 1%, or $0.50.
- Instant payout of the $48.25 on Stripe: 1.5%, or about $0.72.
- With $4 sales tax on Webflow Standard, the 2% applies to $54, so the platform fee becomes $1.08.
| Fee line | Shopify Basic + Shopify Payments | Webflow Standard + Stripe | Webflow Plus + Stripe | systeme.io + Stripe | systeme.io + PayPal Checkout |
|---|---|---|---|---|---|
| Processing (percentage) | $1.45 (2.9%) | $1.45 (2.9%) | $1.45 (2.9%) | $1.45 (2.9%) | $1.75 (3.49%) |
| Processing (fixed) | $0.30 | $0.30 | $0.30 | $0.30 | $0.49 |
| Platform transaction fee | $0.00 | $1.00 (2%) | $0.00 | $0.00 | $0.00 |
| Fees on this sale | $1.75 | $2.75 | $1.75 | $1.75 | $2.24 |
| Plan fee share at 40 sales/month | $0.73 ($29 / 40) | $0.73 ($29 / 40) | $1.85 ($74 / 40) | $0.00 (Free plan) | $0.00 (Free plan) |
| Kept before product, shipping and tax | $47.52 | $46.52 | $46.40 | $48.25 | $47.76 |
When a sale goes wrong
Refunds and disputes are where small stores lose the most per order. Refund the $50 sale above on Stripe and you return $50 but do not get the $1.75 processing fee back, so the refund costs $1.75. A chargeback is worse: on Stripe you lose the $50 while the dispute runs, pay a $15 dispute fee, and pay another $15 if you counter it manually, which is refunded only if you win. On Shopify Payments in the US the chargeback fee is $15 and is returned if you win; Shopify says you usually have 7 to 21 days to respond.
On a $50 order, one lost Stripe dispute costs $50 plus $15 plus the original $1.75. That wipes out the fees saved on dozens of other sales, which is why clear product descriptions, a visible refund policy and a recognisable statement name are worth more than shaving a tenth of a percent off processing.
| Event on a $50 sale | Stripe | Shopify Payments (US) | PayPal |
|---|---|---|---|
| Full refund | Lose $1.75 processing fee | Not stated on the pages we read; check Shopify Payments refund terms | Lose original fees ($2.24 on PayPal Checkout) |
| Chargeback or dispute fee | $15 per dispute | $15, returned if you win | $20 chargeback (card) or $15 dispute (PayPal account) |
| Responding to the dispute | $15 if manual, refunded if you win | No separate fee listed | No separate fee listed |
Break-even points worth knowing
Webflow Ecommerce Plus costs $45 a month more than Standard on yearly billing ($74 versus $29) and removes the 2% transaction fee. 2% of sales equals $45 at $2,250 a month in sales, so below that Standard is cheaper and above it Plus is cheaper, before considering Plus's higher item limit (5,000 versus 500).
On Shopify, the third-party transaction fee is the line to watch. If you keep a third-party provider on Basic, you pay that provider's processing fee plus Shopify's 2%. On $3,000 a month in sales that 2% is $60 a month, more than the $29 plan itself.
- List your expected monthly sales and average order value before comparing plans.
- Divide the fixed fee by your average order: 30 cents is 3% of a $10 order but 0.3% of a $100 order.
- Check where your buyers are; a large foreign share adds 1.5% on Stripe.
- Read each platform's dispute rules before launch, not after the first chargeback.
Questions before you decide
What is the difference between a transaction fee and a processing fee?
The processing fee goes to the card processor, such as Stripe's 2.9% plus 30 cents. A transaction fee is an extra percentage the store platform takes, such as Webflow Ecommerce Standard's 2% or Shopify's third-party fee when you do not use Shopify Payments.
Do I get fees back when I refund an order?
Not from Stripe or PayPal. Both say the original processing fees are not returned, although issuing the refund itself is free. Webflow says there is no fee for issuing a refund from its Orders tab.
How much does a chargeback cost?
Stripe charges $15 per dispute plus $15 if you respond manually, refunded if you win. Shopify Payments charges US stores $15, returned if you win. PayPal lists a $20 chargeback fee on card transactions.
Does systeme.io charge a transaction fee?
Its pricing page says all plans have 0% transaction fees and you accept payments through Stripe or PayPal. You still pay Stripe or PayPal their processing fees.
Sources & verification
Product details and prices can change. Check the linked provider before buying.
- Shopify pricing Accessed 30 Oct 2026
- Shopify Help: Chargebacks and inquiries Accessed 30 Oct 2026
- Shopify Help: Chargeback process Accessed 30 Oct 2026
- Webflow pricing (Ecommerce plans) Accessed 30 Oct 2026
- Webflow Help: Connect a payment provider Accessed 30 Oct 2026
- systeme.io pricing Accessed 30 Oct 2026
- Stripe pricing Accessed 30 Oct 2026
- PayPal merchant fees (US) Accessed 30 Oct 2026
Sources link directly to providers. Product buttons may use separately labeled affiliate links. Read our disclosure.