Shopify charges 2.9% + $0.30 per transaction on the Basic plan using Shopify Payments, with lower rates on higher plans and additional fees for third-party processors.
Shopify tells you what you charged. Craftybase tells you what it actually cost to make. Connect your Shopify store and get real COGS for every product, automatically.
When you make a sale on Shopify, there are two main types of fees that affect how much you actually keep:
1. Payment Processing Fees
If you use Shopify Payments (Shopify's built-in payment processor), you'll pay:
Basic plan: 2.9% + $0.30 per transaction
Shopify plan: 2.6% + $0.30 per transaction
Advanced plan: 2.4% + $0.30 per transaction
2. Third-Party Transaction Fees
If you use a third-party payment provider like PayPal or Stripe instead of Shopify Payments, Shopify charges an additional transaction fee:
Basic plan: 2% additional fee
Shopify plan: 1% additional fee
Advanced plan: 0.5% additional fee
This is on top of whatever fees your payment processor charges - which is why using Shopify Payments usually makes more sense for most sellers.
Real-World Example
Let's say you sell a handmade candle for $50 with $5 shipping on the Basic plan using Shopify Payments:
Total transaction: $55
Payment processing: $55 × 2.9% + $0.30 = $1.90
That's about 3.45% of your sale going to fees
If you used PayPal instead, you'd pay the PayPal fee (~2.9% + $0.30) plus Shopify's 2% transaction fee - potentially doubling your costs.
Frequently Asked Questions
On the Basic plan ($39/month), Shopify charges 2.9% + $0.30 per transaction when you use Shopify Payments. This fee is applied to the total transaction amount, including any shipping charged to the customer. For a $50 sale with $5 shipping, the payment processing fee works out to $1.90 — about 3.45% of the total transaction.
Shopify's transaction fee is an additional charge that applies only when you use a third-party payment processor like PayPal or Stripe instead of Shopify Payments. On the Basic plan, that's an extra 2% per sale; on the Shopify plan it's 1%; on Advanced it's 0.5%. If you use Shopify Payments, this fee does not apply; you only pay the standard payment processing rate.
Each plan has lower payment processing rates in exchange for a higher monthly fee. With Shopify Payments: Basic ($39/mo) charges 2.9% + $0.30; the Shopify plan ($105/mo) charges 2.6% + $0.30; Advanced ($399/mo) charges 2.4% + $0.30. If you use a third-party processor, add the plan's transaction fee on top: 2% (Basic), 1% (Shopify), or 0.5% (Advanced). Higher-volume sellers often save more on fees than they spend on the upgraded plan subscription.
Yes, but only the standard payment processing fee (2.9% + $0.30 on Basic). The separate transaction fee (the extra percentage Shopify adds for using third-party processors) does not apply when you use Shopify Payments. This is why Shopify Payments is usually the more cost-effective choice: you pay one processing rate instead of stacking a processor fee on top of a Shopify transaction fee.
Your real profit margin after Shopify fees is: (Sale price + shipping charged) − payment processing fee − product cost − actual shipping cost, divided by your sale price. The calculator above does this automatically. The most common mistake is forgetting to account for the actual shipping cost you pay — not just what you charged the customer. If you also want to factor in your cost of goods automatically, Craftybase connects to your Shopify store and tracks true COGS per product.
Yes. Shopify's payment processing fee is calculated on the total transaction amount, which includes any shipping you charge the customer. If you sell a product for $50 and charge $5 for shipping, the processing fee applies to the full $55. This is standard across all major payment processors, not just Shopify. If you offer free shipping, the fee only applies to the product price — but your actual shipping cost still comes out of your profit.
Track all your Shopify fees automatically
Craftybase connects to your Shopify store and automatically imports orders, tracks fees, and calculates your true profit on every sale. Stop guessing - know exactly what you're making.
We ♥ to help small manufacturers just like you to become more successful. Please join our newsletter to receive regular updates and actionable tips on how to take your maker business to the next level!