Shopify Fees Explained: What You’ll Actually Pay in 2025

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!)

Understanding Shopify fees

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:

1. Payment processing and Shopify transaction Fees

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.

2. Shopify app costs and third-party tools

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.

3. Shopify subscription fees

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. .

Region-based Shopify tax transaction fees

Sales tax varies widely depending on where you're selling from and who you're selling to:

• United States: Shopify calculates taxes by state, but you’re responsible for collecting, reporting, and remitting. Learn more in Shopify’s U.S. tax guide
• Canada: Sellers must deal with GST/HST, which varies by province. Find more on Shopify’s Canadian taxes
• UK & EU: You need to configure and collect VAT (Value Added Tax), an ecommerce sales tax. Shopify allows you to include in prices and supports VAT reporting
• India: Shopify allows for GST-inclusive pricing and invoice generation, which is mandatory in India

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 - 

Which Shopify subscription plan should you choose?

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:

Basic plan – $39/month

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:

• Online store with unlimited products
• 2 staff accounts
• Basic reports
• Manual order creation
• Discount codes
• Abandoned cart recovery
• Up to 77% shipping discount with Shopify Shipping
• Shopify POS Lite included

Payment fees (using Shopify Payments)

• 2.9% + 30¢ per online transaction
• 2.7% in-person

Ideal for: Ecommerce business owners who are launching their store, working solo or with a tiny team, and want all the essentials without overspending.

Shopify (also known as Grow) plan – $105/month

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:

• 5 staff accounts
• Standard performance reports
• Lower credit card rates
• Up to 88% shipping discount
• Professional reports
• Better international pricing controls

Payment fees:

• 2.6% + 30¢ per online transaction
• 2.5% in-person

Ideal for: Businesses scaling up, needing more user access, better data, and improved shipping rates.

Advanced plan – $399/month

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:

• 15 staff accounts
• Advanced report builder
• Third-party calculated shipping rates
• Custom international pricing per market
• Duties and import taxes estimation
• Priority shipping rates

Payment fees:

• 2.4% + 30¢ per online transaction
• 2.4% in-person

Ideal for: Established businesses with large teams, high order volumes, and a need for granular reporting and flexible international selling.

Shopify plus – Starting at $2,300/month

This plan offers advanced customization, automation tools, priority support, and the ability to manage multiple stores from one dashboard.

Key features:

• Dedicated account manager
• Custom checkout
• High-level automation tools (Shopify Flow)
• Multi-store support
• Unlimited staff accounts
• Lower transaction fees (negotiable)
• B2B features and APIs
• Advanced security and compliance

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. 

Shopify fees breakdown

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. 

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. 

4 practical tips to reduce Shopify fees

Here are four practical tips to help reduce your Shopify fees:

1. Pair automation tools like Webgility with QuickBooks & NetSuite

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 + QuickBooks integration

Webgility integrates easily with QuickBooks Online and QuickBooks Desktop, and automatically syncs orders, fees, taxes, and shipping data from Shopify. 

Key features include:

• Daily sales summaries or order-level sync
• Automatic reconciliation of payouts (like Shopify Payments or Amazon deposits)
• Accurate COGS tracking and inventory updates
• Multi-channel support (if you sell beyond Shopify)

Here’s what NorthStar Bison, a U.S.-based business, shared about their experience using Webgility:

Source

Webgility + NetSuite Integration

For larger businesses, Webgility integrates with NetSuite to unify your ecommerce and ERP systems. With this integration, Shopify sellers can: 

• Sync Shopify transactions to NetSuite in near real time
• Offer support for custom fields, order statuses, and workflows
• Offer advanced inventory and fulfillment tracking
• Provide consolidated reporting across channels

Dan Wells, the owner of Business Loaded, shares their experience on partnering with Webgility: 

Source

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.

2. Stick to Shopify payments

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. 

3. Audit your apps regularly

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:  

• Check app list and costs: Log in to your Shopify admin and head to the Apps section. List all current apps and note what each one does and how much it costs
• Check app usage: If you haven’t opened it in the last month, do you really need it?
• Check duplicate functionality: Got two apps doing the same thing? Pick the better one and unsubscribe the rest
• Cost vs. value: Is that $50/month app generating enough ROI to justify the expense?
• Look for overlap: Sometimes multiple apps solve the same problem, is that the case?
• Remove or downgrade: Cancel apps you don’t need or switch to cheaper/free plans if usage is low
• Document your changes: Write them in a spreadsheet or an accounting automation software so your books stay accurate

4. Choose an annual plan

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.

Final words

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! 

FAQs

What fees does Shopify charge?

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.

How much does it cost to run a Shopify?

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.

How much does Shopify take from a $100 sale?

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.

Is it cheaper to sell on Etsy or Shopify?

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.