Stripe vs PayPal vs Square vs Shopify Payments: US fees compared

Every card payment takes a cut of your revenue before money reaches your bank account. For most new online stores, standard domestic card processing starts at 2.9% + 30¢ per transaction, but monthly fees, dispute costs and in-person rates pull the options apart. This comparison breaks down what Stripe, PayPal, Square and Shopify Payments charge on real orders, how fast they pay out, and which one fits your setup. All figures are US-dollar list prices and terms checked on 2026-10-03.

For the mechanics of payment authorizations, chargebacks and security rules, read our companion guide to online payments, fees and chargebacks.

The four in one table

Worked example: what each processor costs on real orders

All orders below assume domestic US debit or credit cards processed online.

Order fees on a $25, $40 and $100 order

On a $25 purchase, a 19¢ difference in fixed fees shifts your margin immediately:

On a typical $40 order:

On a $100 order:

A month at 30 orders ($1,200 in monthly sales)

A starter store with 30 orders of $40 a month. These are card fees only; your store platform’s plan price comes on top whichever processor you use (Shopify Payments is only available inside a Shopify plan).

Square Free saves $44.20 over Square Plus at this volume. On Shopify Basic, connecting Stripe instead of using Shopify Payments adds Shopify’s 2% third-party fee ($24.00 on $1,200), so card costs rise from $43.80 to $67.80.

The cost of one lost chargeback on a $40 order

Suppose a buyer disputes a $40 item (wholesale product cost $12, outbound shipping $6) and you lose:

• The customer’s bank claws back the full $40.00 sale proceeds.
• The customer keeps the product, so your $12.00 inventory cost is gone.
• The carrier does not refund postage, so your $6.00 shipping cost is gone.
• The processor debits a non-refundable dispute fee: $15.00 on Stripe, or $20.00 on PayPal for card chargebacks.

Your actual out-of-pocket cash loss is $12 (product) + $6 (shipping) + $15 (Stripe dispute fee) = $33.00. On PayPal, with its $20.00 chargeback fee, your cash loss is $12 + $6 + $20 = $38.00.

You also forfeit the expected $40.00 revenue and the $22.00 gross margin you anticipated. After a $1.46 card fee, each normal $40 sale leaves $20.54 ($40 − $12 − $6 − $1.46). One lost Stripe chargeback ($33.00) wipes out the profit of about two sales ($33.00 ÷ $20.54 = 1.6).

Rule of thumb: when flat fees hurt small orders

Payment fees combine a percentage and a fixed cent charge. On small carts, that fixed charge takes a disproportionate bite:

• On a $10.00 order, Stripe or Shopify Payments Basic (2.9% + 30¢) takes 29¢ + 30¢ = 59¢, an effective fee of 5.9%. The 30¢ fixed fee alone represents 3.0% of the entire purchase.
• On PayPal Checkout (3.49% + 49¢), a $10.00 order incurs 35¢ + 49¢ = 84¢, an effective fee of 8.39%. The 49¢ fixed fee alone consumes 4.9% of the order.
• On a $100.00 order, that same 30¢ flat fee is just 0.3% of the sale, and the 49¢ fee is just 0.49%.

Rule of thumb: If your average order value is under $15, flat cent fees will eat your profit margins fast. Bundle low-cost items into multi-packs, introduce a minimum cart size, or steer customers toward payment methods with lower fixed charges.

Run it with your own numbers: Total processor fee = (order total × rate %) + fixed transaction fee Net profit per order = order total - processor fee - product cost - shipping cost

Use our free profit per order calculator to test your exact margins, and read the monthly cost of running an online store to account for hosting, domains and app expenses.

Stripe: for standard card processing with no monthly fee

Stripe’s Standard package charges no setup or monthly gateway fees. You pay 2.9% + 30¢ per successful domestic card transaction, and payouts follow a rolling 2 business day schedule in the US (initial payout scheduled within 7 to 14 days). Instant Payouts cost 1.5% with a 50¢ minimum. Surcharges apply for international cards (+1.5%), currency conversion (+1%), manual card entry (+0.5%), and in-person card payments (2.7% + 5¢).

If a dispute occurs, Stripe debits a $15.00 dispute received fee. If you choose to contest the claim, a $15.00 dispute countered fee also applies, which Stripe refunds if you win. The initial $15 fee is non-refundable. Stripe fits best if you build on website platforms such as Squarespace, Wix or WooCommerce.

Shopify Payments: for selling on Shopify without extra fees

Shopify Payments is Shopify’s built-in processor, eliminating third-party transaction fees. Card rates scale with your plan:

• Basic ($29/month yearly, $39 monthly): 2.9% + 30¢ online domestic; 2.6% + 10¢ in person.
• Grow ($79/month yearly, $105 monthly): 2.7% + 30¢ online domestic; 2.5% + 10¢ in person.
• Advanced ($299/month yearly, $399 monthly): 2.5% + 30¢ online domestic; 2.4% + 10¢ in person.
• Plus (starts at $2,300/month): 2.25% + 30¢ online domestic; 2.3% + 10¢ in person.

Premium cards like American Express cost 3.5% + 30¢ on Basic (3.3% on Grow, 3.1% on Advanced), and foreign cards add +1%. Payouts take 3 business days plus 1 to 3 bank days. If a dispute is filed, the customer’s bank deducts the chargeback fee and disputed amount immediately.

Using an outside gateway like Stripe on Shopify adds a third-party transaction fee: 2% on Basic, 1% on Grow, and 0.6% on Advanced. On Basic, that raises Stripe to 4.9% + 30¢ ($2.26 on a $40 order). Always use Shopify Payments if you sell on Shopify.

Square: for selling in person and online under one roof

Square is built around in-person selling with no monthly software fee on its entry tier. Square Free ($0/month per location) charges 3.3% + 30¢ online and 2.6% + 15¢ in person (tap, dip or swipe). Square Plus ($49/month per location) drops online cards to 2.9% + 30¢ and in-person to 2.5% + 15¢. Premium ($149/month) offers 2.9% + 30¢ online and 2.4% + 15¢ in person. Manual card entry is 3.5% + 15¢ on all plans.

Square offers next business day bank transfers for free, or instant transfers for a fee. It also syncs with Wix online stores. Moving from Free to Plus saves 0.4 percentage points online (3.3% vs 2.9%) but costs $49.00 a month. You must process $12,250 a month in online cards ($49 ÷ 0.004) to cover the fee. Below that, Square Free leaves more cash in your pocket.

PayPal: for buyers who want to pay from a PayPal balance

PayPal lets buyers pay from their PayPal account or as guests. Its online rates are higher than the card-only processors here:

• PayPal Checkout and Guest Checkout: 3.49% + 49¢ (0.49 USD) for domestic transactions.
• Standard credit and debit cards: 2.99% + 49¢ (0.49 USD).
• Point of Sale (in person): 2.29% + 0.09 USD for card-present sales (3.49% + 0.09 USD manual).
• International transactions: An additional 1.50% fee applies to international commercial payments.
• Withdrawals: Standard bank transfers to eligible linked accounts have no fee; instant withdrawals cost 1.50%.

PayPal charges a $20.00 chargeback fee on card disputes, or a $15.00 dispute fee on PayPal transactions (waived under Seller Protection). Buyers have 180 days to dispute, and banks can take 75 days to resolve chargebacks. Because PayPal Checkout costs $1.89 on a $40 order versus $1.46 on Stripe, offer PayPal as a secondary payment button rather than your sole checkout option.

Who should pick something else

• Sellers with fewer than 10 orders a month: If you make only a handful of sales, fixed store builder plans ($29/month) represent a heavy overhead. Selling on established marketplaces like Etsy or Amazon may prove more economical initially. See our analysis in selling on Etsy, Amazon or your own store.
• Businesses selling restricted or regulated products: Every processor publishes a list of businesses it will not support. Read it before you sign up, because an account can be closed after launch.
• Sellers outside the United States: Card rates, dispute fees and payout schedules on this page are US figures. Check each processor’s pricing page for your country.

Common mistakes when choosing a payment processor

• Offering only PayPal Checkout at checkout: Paying 3.49% + 49¢ on every transaction costs $43 more for every 100 orders of $40 compared to Stripe or Shopify Payments. Always offer standard credit card fields alongside digital wallets.
• Using third-party gateways on Shopify: Connecting Stripe or Authorize.net to a Shopify Basic plan adds Shopify’s 2% third-party fee, $20 for every $1,000 in sales.
• Upgrading to Square Plus prematurely: Square Plus costs $49 per month per location. Unless online card sales exceed $12,250 each month, the 0.4% rate reduction does not cover the subscription fee.
• Neglecting statement descriptors: Failing to configure a recognizable billing descriptor (5 to 22 characters matching your store name) makes a charge harder for buyers to recognize on their statement, which can lead to disputes.
• Ignoring international transaction add-ons: If you ship internationally, foreign cards add 1% on Shopify Payments and 1.5% on Stripe or PayPal, plus currency conversion costs. Account for these surcharges in your pricing.

How to decide in five minutes

1. Check your platform: If you build on Shopify, select Shopify Payments. If on Squarespace, Wix or WooCommerce, select Stripe.
2. Review in-person sales needs: If taking payments at pop-up markets or retail counters, evaluate Square Free or Shopify POS.
3. Decide on secondary wallets: Turn on Apple Pay and Google Pay. If your audience uses PayPal, enable PayPal Checkout as an optional secondary button.
4. Calculate your average order fee: Run your average order value through the formula above to ensure your margin covers payment processing.
5. Set up dispute safeguards: Configure clear refund terms, verify order delivery with tracking numbers, and set a recognizable statement descriptor before taking your first live order.

For step-by-step launch guidance, follow our guide to how to open an online store and download our free store launch checklist.

This comparison is general information, not legal or tax advice.

Sources (checked 2026-10-03)

• Stripe: pricing, online and in-person card rates, add-on fees, dispute fees, Instant Payouts
• Stripe Docs: payouts, default settlement timing and initial payout window
• PayPal: business fees (US), Checkout rates, standard card rates, Point of Sale rates, chargeback fees, dispute fees, bank withdrawals
• PayPal Help: what is a chargeback, chargeback definition, 180-day buyer window, 75-day card company resolution timeline
• Square: pricing, Free, Plus and Premium plan pricing, online card rates, in-person rates, bank transfer timing, Wix store sync
• Shopify: pricing, Basic, Grow, Advanced and Plus plan prices, online standard and premium card rates, third-party provider fees, POS Pro add-on
• Shopify Help Center: payments, Shopify Payments, external providers and payment options
• Shopify Help Center: payout timing, Shopify Payments US settlement schedule
• Shopify Help Center: chargebacks, chargeback deduction and fee process