Shopify transaction fees can be confusing—especially if you’re new to eCommerce or switching platforms. You’ve probably asked: “Does Shopify charge transaction fees?”
The short answer? Yes—but it depends.
In this blog, we’ll break down how Shopify transaction fees work, when they apply, and how to reduce them. Plus, we’ll show how tools like PlugBooks.io make managing these costs easier for online store owners.
🔑 Key Things
- Shopify charges transaction fees only when you use third-party payment gateways.
- These fees range from 0.5% to 2.0%, depending on your Shopify plan.
- Shopify Payments users don’t pay transaction fees.
- You still pay payment processing fees (from Stripe, PayPal, etc.), even if transaction fees are waived.
- PlugBooks.io helps you automate tracking, calculate true profit margins, and understand the impact of fees.
📦 PlugBooks.io: Track Every Shopify Fee Without the Hassle
Running an eCommerce store is complex enough — don’t let transaction fees confuse your accounting.
PlugBooks.io is a smart accounting tool designed for Shopify and eBay and Amazon sellers. It syncs all your transactions, including:
- Shopify transaction fees
- Shopify tax transaction fees
- Payment gateway charges
- Refunds, chargebacks, and more
- With real-time insights and clean reports, PlugBooks.io helps you understand where your money is going—so you can focus on growing your store, not managing spreadsheets.
🧾 What Are Shopify Transaction Fees?
Shopify transaction fees are extra charges Shopify applies when you use third-party payment gateways (e.g., PayPal, Stripe) instead of Shopify Payments.
These are different from payment processing fees, which every platform charges. Shopify adds its own transaction fee only when you bypass Shopify Payments.
So if you’re wondering, “Does Shopify charge transaction fees even after paying the monthly plan?” — the answer is yes, if you’re not using Shopify Payments.
💳 Shopify Fees Transaction Breakdown (By Plan)
Here’s a quick look at how Shopify fees transaction charges vary by plan:
| Shopify Plan | Shopify Transaction Fee | If Using Shopify Payments |
| Basic | 2.0% | 0% |
| Shopify | 1.0% | 0% |
| Advanced | 0.5% | 0% |
🟢 Pro Tip: Activating Shopify Payments eliminates these extra fees entirely.
🛍️ Does Shopify Charge Transaction Fees for Every Sale?
Yes, Shopify charges transaction fees if you:
- Use a third-party gateway
- Haven’t enabled Shopify Payments
- Process offline transactions in some regions
If none of these apply, your store may not be affected.
To lower your Shopify fees transaction burden, use Shopify Payments and monitor expenses using tools like PlugBooks.io.
📊 Shopify Tax Transaction Fees: What You Should Know
What about Shopify tax transaction fees?
Shopify doesn’t charge tax on the transaction fee itself. However, you might still pay:
- Sales tax or VAT based on your location
- Additional taxes on your revenue, not the fee
This means tax responsibilities vary by country — be sure to use a tool like PlugBooks.io to track tax-inclusive Shopify fees and stay compliant.
🧠 How to Reduce Shopify Fees Transaction Charges
If Shopify’s fees are eating into your margins, try these steps:
- ✅ Switch to Shopify Payments — it removes transaction fees completely
- 📦 Bundle multiple products into one sale to reduce total transactions
- ⬆️ Upgrade your plan to lower fee percentages
- 💡 Use PlugBooks.io to track exact fee amounts and analyze trends
- 📊 Review your gateway choices — not all processors charge the same rates
Over time, these changes can significantly improve your profit margins.
🔍 Final Thoughts
So, does Shopify charge transaction fees? Yes — but only in specific cases.
And the good news? You can avoid them with a few smart tweaks.Most sellers find that Shopify’s ease of use, powerful features, and integrations make it worth the cost — especially when paired with smart accounting tools like PlugBooks.io.
🙋♂️ Frequently Asked Questions (FAQs)
1. Are Shopify transaction fees charged on each item or total order?They’re applied to the total order amount, not per item.
2. What if I use both Shopify Payments and PayPal—will I be charged?If Shopify Payments is active and the customer chooses PayPal, the Shopify Payment Charges still applies for that order.
3. Do Shopify fees transaction amounts change with currency?No, the percentage stays the same, but conversion rates and international gateway fees may apply.
4. Are There Hidden Shopify Commission Fee Costs?Not exactly, but extra costs like chargeback fees, currency conversion, and third-party app fees can add up quickly.
5. Can I get Shopify to waive my transaction fees?Only if you use Shopify Payments. Shopify does not waive fees for custom arrangements unless you’re on Shopify Plus with a negotiated rate.
6. How does PlugBooks.io help with Shopify Payment Charges management?It pulls data directly from your Shopify store, tracks all Shopify Payment Charges entries (including taxes), and creates easy reports for your accountant or bookkeeper.