Shopify charges you to sell. Not just a monthly subscription — an additional cut of every transaction, every month, forever. Most store owners discover how expensive this is only after they’ve been locked in for a year.
Let’s run the actual numbers, not the marketing page numbers.
How Shopify’s Fee Structure Actually Works
Shopify has three monthly plan tiers: Basic at $39/month, Shopify at $105/month, and Advanced at $399/month. The fee you pay per transaction depends on which plan you’re on — and whether you use Shopify Payments as your processor.
If you use Shopify Payments, the transaction fee is waived. If you use any other payment gateway — Stripe, PayPal, Authorize.net — Shopify charges an additional fee on top of whatever your gateway already charges:
- Basic plan: 2% per transaction
- Shopify plan: 1% per transaction
- Advanced plan: 0.5% per transaction
That sounds like a small number. It isn’t.
The Math on Real Revenue
Marcus runs an outdoor gear store doing $40,000/month in revenue. He’s on the Basic Shopify plan at $39/month and uses Stripe for processing (2.9% + $0.30 per transaction). Here’s what Marcus actually pays:
- Stripe processing: ~$1,220/month
- Shopify transaction fee (2%): $800/month
- Shopify subscription: $39/month
- Total platform cost: $2,059/month — 5.1% of revenue
If Marcus upgraded to the Shopify plan ($105/month), he’d save $400/month on transaction fees but pay $66 more in subscription. Net savings: $334/month. The break-even on upgrading plans is at roughly $13,200/month in revenue, and most store owners don’t do this math until they’re already at scale.
The Shopify Payments Trade-Off
Shopify’s obvious answer to transaction fees is: use Shopify Payments, and the extra charge disappears. That’s true. But it comes with constraints that aren’t always disclosed upfront.
Shopify Payments is built on Stripe’s infrastructure, and it’s only available in 17 countries as of 2025. If you’re outside that list — or in a product category Shopify deems high-risk (CBD, adult content, firearms accessories, certain supplements) — you’re forced to use a third-party gateway. Which means transaction fees, unavoidably.
Also: Shopify Payments can freeze your funds. There are hundreds of documented cases of stores having payouts held for 30–120 days during “account reviews.” When that’s your only gateway, your cash flow stops.
Credit Card Processing Rates: Shopify vs. Third-Party Gateways
Even if you use Shopify Payments and avoid transaction fees, the credit card processing rates aren’t always competitive:
| Plan | Credit card rate (online) |
|---|---|
| Basic | 2.9% + $0.30 |
| Shopify | 2.6% + $0.30 |
| Advanced | 2.4% + $0.30 |
Stripe’s standard rate is also 2.9% + $0.30, with volume discounts available after $80,000/month in processing. Square Online charges 2.9% + $0.30. So Shopify Payments isn’t cheaper than the competition — it just eliminates the extra Shopify fee when you use it.
If you have negotiated rates with a gateway (common for stores doing over $100k/month), you can’t bring those rates to Shopify without paying the transaction fee on top.
Annual Fee Totals by Revenue Level
Here’s what Shopify costs per year across plans, assuming Stripe processing plus Shopify transaction fees:
Store doing $10,000/month ($120k/year):
- Basic + Stripe + 2% fee: ~$7,560/year in platform costs
- Shopify plan + Stripe + 1% fee: ~$5,784/year
- Advanced + Stripe + 0.5%: ~$8,568/year (overkill at this revenue)
Store doing $50,000/month ($600k/year):
- Basic + Stripe + 2%: ~$30,468/year
- Shopify plan + Stripe + 1%: ~$19,860/year
- Advanced + Stripe + 0.5%: ~$19,548/year
At $600k in annual revenue, you’re paying between $20,000 and $30,000/year just in platform and processing overhead — before a single ad dollar, before any staff cost.
What WooCommerce Actually Costs by Comparison
WooCommerce itself is free. You pay for hosting, a payment gateway, and any premium plugins you need. There are no transaction fees taken by WooCommerce.
A realistic annual cost breakdown for a WooCommerce store on managed WordPress hosting:
- Managed hosting (Kinsta, WP Engine, or equivalent): $600–$2,400/year
- Payment gateway (Stripe at standard rates): 2.9% + $0.30 — same as Shopify Payments, but no extra platform fee
- Essential plugins (security, SEO, forms): $200–$500/year
- Total overhead on $600k revenue: ~$18,000–$20,000/year
And that $18k–$20k includes your actual processing costs. The platform overhead itself is under $3,000/year.
Elena moved her cosmetics store from Shopify Basic to WooCommerce after doing exactly this math. At $35,000/month in revenue, she was paying $700/month in Shopify transaction fees alone. After the switch, that cost dropped to zero. The WooCommerce build cost $897 through our fixed-price packages, and she recovered that cost in the first 1.3 months of savings.
The Hidden Costs Shopify Doesn’t Advertise
Transaction fees and subscription costs are visible. These costs are less visible:
App dependency. Shopify’s core product is intentionally limited. Subscription billing, advanced inventory management, custom checkout logic, B2B pricing tiers — all of these require paid apps at $20–$200/month each. A store with six necessary apps can easily add $600–$800/month in app costs.
Theme lock-in. A premium Shopify theme costs $180–$350 once. But customizing beyond what the theme allows requires either liquid templating knowledge or a developer charging $100–$200/hour. You don’t own the theme’s underlying architecture in the same way you own custom-coded files.
Annual price increases. Shopify raised plan prices in 2023. They can raise them again. With WooCommerce, your hosting costs are governed by a competitive market. No single company controls the price.
If you want a direct look at how your current store’s costs compare to alternatives, Honest runs a quick ecommerce audit that surfaces these numbers without a sales call attached.
When Shopify’s Fees Are Worth It
Shopify isn’t always the wrong choice. If you’re doing under $5,000/month in revenue, the simplicity of Shopify’s admin interface and built-in hosting might be worth the fee premium — you’re not losing enough money to justify a platform migration.
If you sell primarily on Shopify POS in physical retail, the unified inventory system has real operational value.
And if you genuinely want zero server maintenance responsibility and are willing to pay for that convenience, Shopify delivers it. The question is whether what you’re paying for it is proportionate to what you get.
FAQ
Does Shopify charge transaction fees if I use Shopify Payments? No. If you use Shopify Payments as your processor, Shopify waives the additional transaction fee. You still pay credit card processing rates (2.9% + $0.30 on Basic), but not the extra 2%, 1%, or 0.5% platform fee.
What happens if my business type isn’t eligible for Shopify Payments? You’ll have to use a third-party gateway and pay Shopify’s transaction fee on every sale. There’s no workaround — it’s baked into the Terms of Service.
Can I negotiate Shopify’s transaction fees? Not as a standard merchant. Shopify Plus (the enterprise tier at $2,500/month or 0.25% of revenue, whichever is higher) reduces transaction fees to 0.15% for third-party gateways. For most SMBs, Plus doesn’t make financial sense.
Is WooCommerce actually free? The core plugin is free and open-source. You’ll pay for hosting, a payment gateway, and any premium extensions you need — but none of those costs go to WooCommerce. You’re paying vendors in a competitive market, not a single platform that controls pricing.
How long does it take to migrate from Shopify to WooCommerce? Product data, customer records, and order history can be migrated with tools like Cart2Cart or LitExtension. A clean migration for a store with 500–2,000 products typically takes 2–4 weeks including testing. Our custom WooCommerce development includes migration scoping if that’s the direction you’re heading.
At what revenue level does WooCommerce become clearly cheaper than Shopify? For stores using third-party payment gateways, WooCommerce becomes cheaper almost immediately because you avoid the platform transaction fee entirely. For stores using Shopify Payments, the break-even depends on your app costs and hosting comparison — but typically becomes clear above $15,000/month in revenue.