The True Cost of Shopify at Scale: When $29/Month Becomes $2,000

Shopify's marketing is brilliant. "Start selling for just $39/month" sounds like a bargain — until you're six months in and your actual bill is closer to $300. The uncomfortable truth is that Shopify is too expensive for the majority of growing stores once you account for apps, transaction fees, theme costs, and the inevitable push towards Shopify Plus. What starts as a simple $39/month subscription quietly balloons into $1,500-5,000 per year, and by the time you notice, you're locked into an ecosystem that makes migration painful.

This isn't speculation. It's basic maths that Shopify's own pricing page makes deliberately hard to calculate. Let's break down every hidden cost, compare it honestly against self-hosted alternatives, and help you decide whether Shopify is actually worth what you're paying.

Shopify's pricing tiers: what they actually include

Shopify offers four main plans, and on paper the pricing looks straightforward. In practice, every tier is designed to push you towards the next one by gating features you'll inevitably need.

Basic ($39/month) — Two staff accounts, basic reports, up to 77% shipping discount. You get a functional storefront, but you're immediately hit with 2% transaction fees on any payment gateway that isn't Shopify Payments. No professional reports, no third-party calculated shipping rates, no ecommerce automations.

Shopify ($105/month) — Five staff accounts, standard reports, up to 88% shipping discount. Transaction fees drop to 1%, and you get basic automations. Still no advanced report building or third-party calculated shipping at checkout.

Advanced ($399/month) — Fifteen staff accounts, custom report builder, third-party calculated shipping, and transaction fees reduced to 0.5%. This is where most scaling stores end up because the Basic and Shopify plans simply don't have the reporting or shipping features needed to run a serious operation.

Plus ($2,300/month) — Enterprise tier with checkout customisation, Shopify Functions, wholesale channel, and dedicated support. We'll cover this in detail below, because it's where Shopify's pricing truly becomes eye-watering.

The app tax

Here's where Shopify's real cost structure reveals itself. The platform deliberately keeps core functionality minimal so that you're forced into their app ecosystem. The average Shopify store runs 6-8 paid apps, each costing between $15 and $80 per month. These aren't optional luxury add-ons — they're basic features that most other platforms include out of the box.

A typical app stack for a growing store looks like this: a reviews app (Judge.me or Loox at $15-50/mo), email marketing integration (Klaviyo at $20-150/mo depending on list size), upsell and cross-sell tools ($20-50/mo), a loyalty or rewards programme ($20-60/mo), an SEO app ($20-40/mo), and a backup solution ($5-15/mo). That's $100-365 per month in apps alone — on top of your Shopify subscription.

The app dependency creates a compounding problem. Each app adds its own JavaScript to your storefront, slowing page loads. Each app is a separate subscription that can increase pricing at any time. And each app stores data in its own format, making migration progressively harder. You're not just paying for functionality — you're paying for vendor lock-in disguised as convenience.

Transaction fees add up fast

Shopify charges transaction fees on every sale unless you use Shopify Payments as your payment processor. On the Basic plan, that's 2% of every transaction. On Shopify, 1%. On Advanced, 0.5%. These are on top of the credit card processing fees you're already paying.

Even if you do use Shopify Payments (which isn't available in every country), you're still paying credit card processing fees: 2.9% + 30c on Basic, 2.6% + 30c on Shopify, and 2.4% + 30c on Advanced. These rates are competitive but not exceptional — Stripe charges the same 2.9% + 30c without locking you into a specific platform.

Let's do the maths. A store doing $500,000/year in revenue on the Shopify plan (not using Shopify Payments) pays 1% in transaction fees — that's $5,000 per year going straight to Shopify before credit card processing. Even on the Advanced plan at 0.5%, that's still $2,500 per year. On the Basic plan at 2%, you're handing over $10,000.

Theme and customisation costs

Shopify's free themes are functional but generic. If you want a professional-looking store that stands out, you're looking at a premium theme from the Shopify Theme Store ($300-400) or a third-party marketplace ($180-350). Unlike WordPress themes, Shopify themes are built with Liquid — a proprietary templating language that severely limits what you can do without developer help.

Customising a Shopify theme beyond what the drag-and-drop editor allows means hiring a Liquid developer, and they don't come cheap. Experienced Shopify developers charge $100-200/hour, and even seemingly simple changes (custom product page layouts, unique collection filters, checkout modifications) can take 5-20 hours of development time.

The customisation ceiling is what ultimately pushes many stores towards Shopify Plus. Want to customise the checkout? Plus only. Want to add custom scripts that run server-side? Plus only. Want to create automated workflows that go beyond basic templates? You guessed it — Plus only.

Shopify Plus: when $2,300/month is the floor

Shopify Plus is positioned as the enterprise solution, but in reality, many stores end up there not because they're enterprise-scale but because they've hit the customisation limits of the standard plans. The minimum is $2,300/month (billed annually), but the actual cost depends on your revenue — Shopify Plus charges a percentage-based fee once you exceed certain thresholds.

The features that drive stores to Plus are telling: checkout customisation (the single most impactful conversion optimisation you can make), Shopify Functions (server-side logic for discounts, shipping, and payments), Script Editor for custom pricing rules, and the wholesale channel for B2B sales. These are features that WooCommerce and most other platforms offer for free or via one-time plugin purchases.

Beyond the base subscription, Plus stores face additional costs: Shopify Functions development ($5,000-20,000 for custom implementations), Plus-specific app pricing (many apps charge 2-5x more for Plus stores), and agency partners who specialise in Plus builds ($50,000-200,000 for a full implementation). The total cost of ownership for a Shopify Plus store easily exceeds $50,000/year.

The real cost comparison

To understand whether Shopify is genuinely overpriced, we need to compare it fairly against the leading alternative: self-hosted WooCommerce. Here's an honest breakdown of what each platform delivers and where each falls short.

The pattern is clear: Shopify excels at getting you started quickly but becomes progressively more expensive and restrictive as your store grows. For stores doing under $100k/year where simplicity is the priority, that trade-off might be acceptable. For stores scaling beyond that, the economics tilt decisively towards self-hosted solutions.

Self-hosted WooCommerce: what it actually costs

WooCommerce itself is free, open-source software. But "free" doesn't mean zero cost — you need hosting, a domain, and potentially some premium plugins. The critical difference is that these costs are predictable, don't scale with your revenue, and don't involve platform transaction fees.

Hosting: $25-100/month. Managed WordPress hosts like Cloudways ($25-50/mo) or Kinsta ($35-100/mo) provide excellent performance with automatic backups, staging environments, and server management. Unlike Shopify, your hosting cost stays the same whether you're doing $10k or $1M in revenue.

Domain: $12/year. Identical across platforms. Nothing hidden here.

Payment processing: Stripe at 2.9% + 30c. This is the same rate as Shopify Payments, but without any additional platform transaction fee on top. You can also use PayPal, Square, or any other processor without penalty — WooCommerce doesn't charge extra for using a third-party gateway.

Plugins: mostly free, premium ones are typically one-time purchases. WooCommerce's plugin ecosystem is fundamentally different from Shopify's app model. Core functionality like SEO (Yoast, free), caching (WP Super Cache, free), email (WooCommerce email, free), and reviews (built-in) comes at no extra cost. Premium plugins for advanced features like subscriptions or bookings are usually $79-199 as a one-time purchase with a year of updates, not $30-80/month forever.

The total picture: A well-configured WooCommerce store costs $300-1,200/year in hosting plus one-time plugin purchases. Compare that with Shopify's $1,500-5,000/year in recurring subscription, app, and transaction fees. Over three years, a growing store saves $3,500-15,000 by self-hosting — and that gap only widens as revenue increases because WooCommerce has no revenue-linked fees. For a deeper breakdown, see our complete guide to headless WooCommerce costs.

Headless WooCommerce: the cost-performance sweet spot

If you want the best of both worlds — WooCommerce's cost efficiency and open-source flexibility combined with the blazing-fast frontend performance that Shopify stores struggle to achieve — headless WooCommerce is the answer. The concept is straightforward: keep WooCommerce as your backend for managing products, orders, and inventory, but replace the traditional WordPress theme with a modern Next.js frontend. If you're new to this approach, our introduction to headless WooCommerce covers the fundamentals.

Backend hosting: $25-50/month. Your WordPress + WooCommerce backend only needs to serve API requests, not render pages for visitors. This means you can use a smaller, cheaper hosting plan than a traditional WooCommerce store would require.

Frontend hosting: free to $20/month. Vercel's free tier is more than sufficient for most stores. Your Next.js frontend is deployed globally on edge servers, delivering sub-second page loads without any CDN configuration.

The headless approach eliminates the two biggest cost drivers of Shopify: transaction fees and app subscriptions. Features that would cost $50-150/month in Shopify apps (product filtering, mega menus, upsells, custom layouts) are built directly into the Next.js frontend at zero recurring cost. The only ongoing expense is hosting — typically $25-70/month total. For a detailed performance comparison, see WooCommerce vs Shopify performance benchmarks.

When Shopify IS the right choice

This article has been critical of Shopify's pricing, but intellectual honesty requires acknowledging the scenarios where Shopify genuinely makes sense. Not every store owner should self-host, and pretending otherwise would be disingenuous.

Non-technical founders who need to launch fast. If you have zero technical knowledge, no development budget, and need a store live this week, Shopify is hard to beat. The trade-off is cost efficiency for speed of launch, and for some businesses that's the right call. You can always migrate later once revenue justifies the investment.

Stores under $100k/year where simplicity matters more than cost. At lower revenue levels, the absolute dollar difference between Shopify and self-hosted solutions is smaller. If your time is better spent on marketing and product development than platform management, Shopify's all-in-one approach has genuine value.

The key question isn't "is Shopify bad?" — it's "is Shopify worth what you're paying relative to what you need?" For many growing stores, the answer is increasingly no.

The bottom line

Shopify is too expensive for the growing majority of ecommerce stores that have moved past the launch phase. The platform's true cost isn't the $39-399/month subscription — it's the compounding effect of app fees, transaction charges, theme limitations, and the revenue-linked pricing that extracts more money the more successful you become. A store doing $500k/year in revenue can easily spend $15,000-20,000 annually on Shopify, while the same store self-hosted on WooCommerce would pay a fraction of that.

The alternative isn't to go without. Self-hosted WooCommerce — especially with a headless frontend — delivers equivalent or superior functionality at $300-1,200/year. No transaction fees beyond your payment processor. No recurring app taxes. No vendor lock-in. No artificial ceiling that forces you onto a $2,300/month enterprise plan just to customise your checkout.

If you're already feeling the squeeze of Shopify's escalating costs, start by auditing your actual spend — subscription, apps, transaction fees, and developer costs combined. Then compare that number against the real cost of headless WooCommerce. For a head-to-head feature comparison, see our WooCommerce vs Shopify performance guide. And if you're ready to explore what owning your own ecommerce stack looks like, our self-hosted ecommerce guide walks you through everything you need to know.