You might still be new to Shopify or knee-deep in Shopify sales and product pages, figuring out what you’ll end up paying can get confusing.
You might be wondering: What are Shopify merchant fees? Which plan makes the most sense for your store right now? Should you upgrade, or are those extra tools just burning a hole in your pocket?
This guide is here to clear it all up. From subscription costs to the Shopify app charges, we’ll break down what selling on Shopify really costs. (along with tips to reduce them, like using Shopify accounting software so you can budget smart and skip those sneaky surprises!)
Say a customer places a $100 order on your Shopify store. On the surface, it looks like a solid sale. But when you factor in Shopify’s built-in fees, app charges, and taxes, that $100 starts to shrink fast.
Here’s where your revenue goes:
If you use Shopify Payments, you’ll be charged 2.9% + 30¢ per transaction on the Basic Shopify plan. So for a $100 order, that’s $3.20 gone right away.
If you’re not using Shopify Payments, you’ll incur an additional Shopify transaction fee, up to 2%, depending on your plan. These fees apply even before you factor in shipping, product costs, or taxes.
On average, apps can add $0.50 to $2+ per order, depending on usage. Since many are billed monthly, their impact on profitability often goes unnoticed until you audit your expenses.
Whether you’re on the Basic ($39/month), Shopify ($105/month), or Advanced ($399/month) plan, this monthly fee should be factored into your per-order profitability, especially if your store is just starting.
We’ve mentioned the full pricing breakdown later in the article. .
Sales tax varies widely depending on where you're selling from and who you're selling to:
Note: Some taxes and shipping fees may not be refundable if a customer cancels or returns an order.
So, a $100 sale on Shopify quickly drops to around $96.30 after processing and app fees (that’s before you factor in shipping, COGS, or your time!).
Now that you know how the fees might stack up -
Choosing the right Shopify plan depends on your business size, sales volume, and the features you need.
Here's a breakdown of each plan to help you decide:
This is one of the most budget-friendly Shopify plans, offering all the essentials to start and run your online store. You can list an unlimited number of products, enjoy unlimited bandwidth, and receive a free SSL certificate to keep your site secure and trustworthy.
Key features:
Payment fees (using Shopify Payments)
Ideal for: Ecommerce business owners who are launching their store, working solo or with a tiny team, and want all the essentials without overspending.
This plan builds on the Basic tier by offering all its features plus superior tools to help you grow. You get access to standard reports that provide deeper insights into sales trends and customer behavior to help you make smarter business decisions as you scale.
Key features
Everything in Basic, plus:
Payment fees:
Ideal for: Businesses scaling up, needing more user access, better data, and improved shipping rates.
This plan includes advanced features, such as a custom report builder and support for up to 1,000 inventory locations. You’ll also benefit from the lowest transaction fees and powerful analytics tools, making it easier to expand into international markets and manage complex operations.
Key features:
Everything in the Grow plan, plus:
Payment fees:
Ideal for: Established businesses with large teams, high order volumes, and a need for granular reporting and flexible international selling.
This plan offers advanced customization, automation tools, priority support, and the ability to manage multiple stores from one dashboard.
Key features:
Ideal for: Enterprise players who need scale, support, and complete control over customization and integrations.
Once you decide on the best Shopify plan, you need to know about the extra fees the platform charges.
To make sense of what you’re paying on Shopify, here’s a quick breakdown of the different types of fees you’ll come across in detail.
|
Fee Type |
Description |
Amount |
Purpose |
|
Subscription fee |
Monthly cost for using Shopify's platform |
$39 (Basic) / $105 (Shopify) / $399 (Advanced)/ $2,500 (Shopify Plus) |
Access to Shopify’s ecommerce tools and features |
|
Shopify transaction fees |
Charged if using external payment gateways (not Shopify Payments) |
2.0% (Basic) / 1.0% (Shopify) / 0.5% (Advanced) |
Fee for not using Shopify Payments |
|
Shopify payments fee |
Credit card processing fee (if Shopify Payments is used) |
2.9% + 30¢ per transaction (Basic Plan, US) |
Fee to process payments via Shopify’s built-in gateway |
|
Shipping label fees |
Cost of purchasing shipping labels through Shopify |
Varies by carrier and package weight/destination |
Simplifies order fulfillment with discounted shipping rates |
|
Theme/Template fees |
Cost for premium store themes |
$350 one-time |
Design customization for your storefront |
|
Shopify app fees |
Monthly cost for using third-party or Shopify apps |
$0 – $100+ per app/month |
Add features like email marketing, reviews, upsells, etc. |
|
Domain fee |
Custom domain registration fees (optional) |
On an average $10-20/year |
Brand your store with a custom domain |
|
Email marketing |
Shopify Email is free up to 10,000 emails/month, then $1 per 1,000 extra |
Variable |
Send campaigns to customers directly from Shopify |
|
POS hardware (optional) |
For in-person selling through Shopify POS |
Basic kit starts at $49 |
Sell products in physical stores or pop-ups |
Say you start on a $39 plan, add paid apps, themes, and pay transaction fees. And suddenly you're spending over $150/month without realizing it. So it’s only natural to wonder if there’s a way to reduce these costs from stacking up.
Here are four practical tips to help reduce your Shopify fees:
Webgility is an automation tool built for ecommerce sellers using platforms like Shopify. It connects your store to accounting tools like QuickBooks and NetSuite, syncing your orders, fees, and payouts automatically, so you’re not stuck juggling spreadsheets.
How does it benefit your business? With less manual work and cleaner books, you dodge tax surprises, skip costly errors, and spend way less on accounting help.
Whether you’re using QuickBooks or NetSuite, you can integrate it with both.
Webgility integrates easily with QuickBooks Online and QuickBooks Desktop, and automatically syncs orders, fees, taxes, and shipping data from Shopify.
Key features include:
Here’s what NorthStar Bison, a U.S.-based business, shared about their experience using Webgility:
For larger businesses, Webgility integrates with NetSuite to unify your ecommerce and ERP systems. With this integration, Shopify sellers can:
Dan Wells, the owner of Business Loaded, shares their experience on partnering with Webgility:
How does this help reduce Shopify fees per sale?
Say you make a $100 sale.
At first glance, this may feel like a win, but behind the scenes, things add up. Shopify takes around $3.20 in transaction fees, you offer free shipping that costs $6, and your upsell app charges $1. If you manually log sales, you might record the full $100 as revenue. (meaning you could pay taxes on income you never actually earned).
Multiply this number by 100 and imagine how much you’d be paying as tax.
Instead, if you use Webgility with QuickBooks or Netsuite, every sale gets synced with all its hidden costs: transaction fees, shipping charges, and app costs. So instead of overstating income, your books reflect the real profit: closer to $89.80. This kind of visibility is one of the Shopify accounting best practices that actually helps you make smarter, more profitable decisions with every sale.
When you opt for Shopify Payments, it can eliminate additional transaction fees that Shopify imposes when using third-party payment gateways. For example, on a $100 sale using PayPal or Stripe, you'd pay around $5.20 in total fees ($3.20 to the processor and $2 to Shopify). But if you switch to Shopify Payments, you avoid that extra 2% fee and only pay the standard 2.9% + 30¢ (about $3.20), saving $2 per sale.
Shopify offers over 100 built-in tools and features across categories like marketing, inventory, order management, etc. So it's easy to forget about that extra $10 you invested in an email tool months ago.
Doing a monthly app audit helps you spot and remove these costs.
Here’s what to look for:
If you're committed to running your store long-term, switch from a monthly to an annual Shopify plan for instant savings. For instance, the Basic Shopify plan costs $39/month if paid monthly, but only about $29/month when billed annually, saving you roughly $120 a year.
For higher-tier plans, the savings are even greater. With a simple switch, you can free up cash that you can reinvest in marketing, inventory, or tools to grow your business.
Shopify gives you the freedom to build your brand your way without a middleman and marketplace rules. But if you're not careful, that freedom can lead to a web of fees, manual accounting, and back-office chaos.
With Webgility, you can automate your bookkeeping, sync Shopify data to your accounting software, and manage fees, taxes, and payouts. Get started for free to enjoy the perks of selling directly without the operational overwhelm!
Shopify charges a monthly subscription starting at $5 if you want to sell only through social media or messaging apps. You’ll also pay transaction fees unless you use Shopify Payments and additional costs, including premium themes, apps, and third-party payment gateways.
Basic plans start at $5/month, but your total cost depends on extra apps, themes, and payment processing fees. Most small businesses spend between $50–$150/month, depending on features and traffic.
If you use Shopify Payments, they take 2.9% + 30¢, which is $3.20 on a $100 sale. If you use a different payment gateway, you may incur extra transaction fees.
Etsy has lower upfront costs, making it cheaper for beginners. However, Shopify gives you more control, customization, and lower fees as your sales grow. So it’s better suited for growing ecommerce brands.