Shopify processing fees are a major part of the ongoing cost of running an online store, but the actual amount paid can be higher than the advertised rate. Factors such as average order value, refund volume, payment methods, and total sales can all affect how much a store spends on payment processing. This guide explains how Shopify processing fees are calculated, how rates differ across subscription plans, and why high-volume merchants may benefit from negotiated pricing.
What are Shopify processing fees?
Shopify processing fees are the card rate you pay when Shopify Payments processes an online or in-person sale: a percentage of the order plus a small fixed amount. They are separate from your subscription and from the third-party transaction fee, which is an extra charge Shopify adds only when an outside payment provider handles the order. If those two terms keep blurring together, our explanation of Shopify transaction fees separates them with examples.
For standard US cards, the processing fee by plan is:
| Payment type | Basic | Grow | Advanced | Plus |
|---|---|---|---|---|
| Online standard card | 2.9% + 30¢ | 2.7% + 30¢ | 2.5% + 30¢ | 2.25% + 30¢ |
| In-person card | 2.6% + 10¢ | 2.5% + 10¢ | 2.4% + 10¢ | 2.3% + 10¢ |
| Processing savings per $10,000 of online sales, compared with Basic | Baseline | $20 | $40 | $65 |
The last row matters for planning. Because the fixed 30¢ is the same on every plan, moving up a tier saves 0.2, 0.4, or 0.65 percentage points on each dollar of sales, not on each order. Whether that justifies a higher subscription is a volume question, which our plan comparison walks through.
Where a processing fee goes
A card processing fee is not one charge. Shopify’s own guide to credit card processing fees breaks it into three layers: interchange, which goes to the customer’s card-issuing bank; assessments, which go to the card network; and the processor’s markup. Shopify Payments is powered by Stripe and uses a flat-rate model, so the three are combined into one price and you do not see them on your statement.
Shopify’s guide illustrates the split with a $100 sale. This is a general example of how fees decompose, not what Shopify Payments charges:
| Component | Who receives it | Illustrative amount on $100 |
|---|---|---|
| Interchange (1.5% + 10¢ in the example) | Card-issuing bank | $1.60 |
| Network assessment (0.14%) | Card network | $0.14 |
| Processor markup | Payment processor | $0.50 |
| Total | $2.24 |
The practical point is that interchange is the largest piece and varies by card type. Premium and rewards cards cost more than basic debit cards. A flat rate hides that variation by charging every card the same price, which is why it is predictable at small volume and why very large merchants sometimes want a different arrangement.
Flat-rate vs Interchange-plus
The two pricing models trade simplicity for transparency:
| Flat rate | Interchange-plus | |
|---|---|---|
| How you are charged | One blended percentage plus fixed fee | Actual interchange and assessments plus a disclosed markup |
| Cost by card type | Same for every card | Varies with the card |
| Predictability | High | Lower, because costs track your card mix |
| Who benefits most | Small and mid-size stores | High-volume merchants with a favorable card mix |
| Shopify Payments | Used for published plan rates | Not published; Plus rates are arranged with Shopify |
One 2026 analysis estimates that merchants moving from flat-rate to interchange-plus pricing can save 50 to 80 basis points once card volume passes roughly $1 million a month, but that figure comes from a third party and is based on Stripe-style pricing, not Shopify’s contracts. Treat it as a reason to ask, not as a promise.
For a store that leaves Shopify Payments to chase a lower rate, Shopify’s third-party fee has to be counted. The all-in rate an outside provider must beat is your Shopify Payments rate minus that fee: 1.9% on Advanced (2.5% minus 0.6%) and 2.05% on Plus (2.25% minus 0.2%). Our guide to Shopify Payments fees shows the full calculation, including the lower thresholds for Basic and Grow.
Six levers that lower Shopify processing charges
Most of the fee is fixed by your plan, but six levers move your real cost.
1. Raise your average order value
The 30¢ fixed amount takes a smaller share of a bigger order. On Basic, a $40 order has an effective rate of 3.65% (2.9% plus 0.75% from the fixed fee), while a $60 order is 3.40%. For a store selling $20,000 a month, lifting the average order from $40 to $60 cuts monthly fixed fees from $150 to about $100, saving roughly $50 a month, or $600 a year.
2. Upgrade only when the processing savings beat the extra subscription cost
Use the savings row in the first table. At $10,000 of monthly sales, Grow saves $20 in processing compared with Basic, Advanced saves $40, and Plus saves $65. If the extra subscription cost is higher than that saving at your volume, an upgrade is a features decision, not a savings one.
3. Reduce refunds
Shopify says card processing fees are not returned when you refund an order. Take a Basic store with $20,000 in monthly sales and an 8% refund rate, which is an illustrative figure. Refunds of $1,600 across 20 orders still leave you paying about $52.40 in lost processing fees every month, or roughly $629 a year. Better size guidance, clearer product photos, and accurate delivery times all reduce that waste.
4. Prevent chargebacks
A lost chargeback costs the disputed amount plus a $15 fee for US stores, and Shopify returns the fee only if you win. Prevention is cheaper than disputing: clear descriptors on statements, reliable tracking, and a visible returns policy.
5. Be deliberate about higher-cost payment methods
Wallets such as Shop Pay, Apple Pay, and Google Pay run at your plan’s normal card rate, so they cost you nothing extra. PayPal Wallet through Shopify Payments starts at 3.49% + 49¢, and Shop Pay Installments carries a higher, unpublished rate. On an $80 order on Basic, PayPal from $3.28 compares with $2.62 for a card, an extra 66¢. If one in five of 250 monthly orders uses PayPal, that adds about $33 a month. Offering these methods can still raise conversion, so compare the cost with the benefit rather than removing them.
6. Revisit your pricing at scale
Standard plans use published rates. If your sales have grown into Plus territory, ask Shopify’s sales team about card rates, and compare any outside provider against the all-in break-even in the previous section rather than its headline rate.
Conclusion
Shopify processing fees are predictable once you know what drives them: a flat rate set by your plan, a fixed fee that punishes small orders, and exceptions such as refunds, disputes, and higher-cost payment methods. Most stores save more by raising order value and reducing refunds than by chasing a different processor. Measure your effective rate regularly, and revisit the question of pricing only when your volume justifies a conversation.
For Shopify stores looking for a professional invoice solution that’s easy to customize without any coding, Vify Shopify Order Printer app is worth considering. Try it for free today and see how it fits your store’s needs.
FAQs
What are Shopify processing fees?
They are the card rates you pay when Shopify Payments processes a sale. For standard US online cards, the rate is 2.9% + 30¢ on Basic, 2.7% + 30¢ on Grow, 2.5% + 30¢ on Advanced, and 2.25% + 30¢ on Plus.
How much are Shopify processing fees per transaction?
On a $100 standard online card sale, the fee is $3.20 on Basic, $3.00 on Grow, $2.80 on Advanced, and $2.55 on Plus. Premium cards, international cards, and currency conversion can add to that.
What is the difference between processing fees and transaction fees on Shopify?
Processing fees are the card rates charged on payments handled by Shopify Payments. The transaction fee is an extra charge Shopify applies when an outside payment provider processes the order. With Shopify Payments you avoid the transaction fee but still pay the processing fee.
Are Shopify processing fees refunded when I refund an order?
No. Shopify says credit card transaction fees are not returned when you issue a refund, and the currency conversion fee is not returned either.
Does Shopify charge processing fees on PayPal or manual payments?
PayPal charges its own rate, which starts at 3.49% + 49¢ in the US. Manual payment methods such as cash, cash on delivery, and bank transfer carry no Shopify processing fee.