Shopify vs custom e-commerce: what it really costs over three years

The short answer

Start on Shopify unless you can name a specific requirement it cannot meet. Shopify handles hosting, security, checkout and payments, and real-user data from the HTTP Archive shows 76.5% of Shopify origins had good Core Web Vitals on mobile in August 2026, against 53.0% for the web as a whole. That is a strong default for a small or mid-sized store.

A custom store makes sense when the way you sell is the product: complex B2B pricing, quotes and approvals, configurable products with your own rules, deep ERP or inventory integration, marketplaces, or a customer experience that templates cannot deliver. In those cases the extra cost buys something Shopify apps would only approximate.

Between the two sit WooCommerce, which is open source and self-hosted, and headless Shopify, where Shopify runs the back end and a custom front end sits on top.

Shopify plans and payment fees

Shopify charges a monthly plan plus card processing on each sale. With Shopify Payments there is no additional transaction fee. If you use a third-party payment provider instead, Shopify adds a fee of 2% on Basic, 1% on Grow, 0.6% on Advanced and 0.2% on Plus, on top of what that provider charges.

In Canada, American Express, international cards and a few other methods are billed at 3.5% plus 30 cents on all plans. In-person Interac payments cost 15 cents on Basic, Grow and Advanced.

Canadian figures from Shopify's pricing page as displayed in Canada on September 28, 2026. US figures as reported by Commerce-UI (2026), because Shopify's page displayed Canadian prices from our location. In euros, Shopify sets prices per country: check its pricing page from your own country.

App costs: the line most budgets miss

Shopify's plan covers the core store; reviews, subscriptions, advanced search, bundles, loyalty, B2B pricing and many marketing tools come from paid apps. App fees are monthly and they grow with the store, so they belong in any multi-year comparison.

Eightx estimated in June 2026, from a Storeleads panel of about 3.59 million active stores, that monthly app spend typically runs US$50 to US$300 for stores under US$1 million in revenue, US$1,000 to US$3,500 between US$1 million and US$5 million, and US$5,000 to US$15,000 between US$5 million and US$20 million. The author describes these as modelled estimates, directional within roughly 25%.

• List the apps you need before choosing a plan, with their price at your expected order volume.
• Check whether an app's feature is already included in a higher plan.
• Uninstall apps you no longer use: many leave scripts behind that slow the store.
• When app spend exceeds what a one-time custom feature would cost over two or three years, compare the two.

WooCommerce: the middle option

WooCommerce is a free, open-source plugin for WordPress with no platform fee and no revenue share. You pay for hosting, which WooCommerce itself puts at US$25 to US$350 a month for most stores, and for extensions at US$29 to US$299 a year each. With WooPayments, standard cards cost 2.9% plus 30 cents in Canada and the US, and 1.5% plus €0.25 in France, with no extra fee if you choose another payment provider.

The trade-off is responsibility. You or your provider handle updates, security, backups and performance. Real-user data shows the risk: in August 2026, only 39.5% of WooCommerce origins had good Core Web Vitals on mobile, against 76.5% for Shopify. WooCommerce suits a store that already lives on WordPress, needs content-heavy pages, or wants to avoid platform fees, and has someone to maintain it.

Headless Shopify: custom front end, Shopify back end

Headless means Shopify keeps the catalogue, checkout, payments and orders, while the storefront customers see is a separate custom application. Shopify provides Hydrogen, a set of components and utilities for building with its APIs, and Oxygen, its serverless hosting for Hydrogen storefronts. Shopify states that Oxygen is available at no extra charge on paid plans.

Headless gives full design and content freedom while keeping Shopify's checkout and admin. It also means you now maintain a custom application: every theme app you relied on may need a custom replacement, and speed is your job. Sites detected as using Next.js, a common headless framework, passed Core Web Vitals on mobile only 35.1% of the time in the same HTTP Archive data. Headless pays off for brands with strong content, several markets, or a store embedded in a larger digital product.

What a custom store costs

Custom e-commerce costs vary more than any other web project. Clutch's e-commerce pricing guide, updated September 21, 2026, reports that most projects on its platform cost under US$10,000, but the average is US$51,943 over about nine months, pulled up by large builds. Those figures mix platform setups and fully custom work.

At ZeniTech, an e-commerce site starts at CA$12,000 (approx. US$8,470 or €7,449) and custom software at CA$15,000, before taxes, with hosting and maintenance at CA$150 a month and out-of-scope work at CA$125 an hour. The code, domain and hosting are in the client's name. A fully custom store with integrations, B2B rules or several markets costs more than the starting price; we quote it at a fixed price once the scope is written.

On a custom store you also pick a payment processor. Stripe's standard rate in Canada is 2.9% plus CA$0.30 for domestic cards, plus 0.8% for international cards and 2% when currency conversion is needed. Stripe says custom pricing with volume discounts is available for large volumes.

3-year total cost at three revenue levels

This is ZeniTech's arithmetic, not a quote, and it is meant to show which costs dominate. Assumptions: average order of CA$100; all sales online with domestic cards; Shopify Payments on the Shopify side and Stripe standard pricing on the custom side; annual Shopify billing; taxes excluded; initial Shopify store setup excluded, since it ranges from DIY to a full agency project.

• Level 1, CA$60,000 a year (600 orders): Shopify Basic, apps assumed at CA$100 a month. Custom store at CA$12,000 plus CA$150 a month maintenance.
• Level 2, CA$300,000 a year (3,000 orders): Shopify Grow, apps CA$300 a month, 20 hours a year of theme work. Custom store at CA$12,000, maintenance, 40 hours a year of development.
• Level 3, CA$1.5 million a year (15,000 orders): Shopify Advanced, apps CA$1,500 a month, 40 hours a year of theme work. Custom store assumed at CA$40,000, maintenance, 80 hours a year of development. All extra hours at CA$125.

Plan and card rates from Shopify (Canada) and Stripe (Canada) pricing pages, September 2026. App assumptions sit inside the Eightx ranges converted to CAD. USD at 1.4168 CAD per USD. Two lessons: card processing is the largest cost at every level, and at CA$1.5 million a 0.5-point better processing rate is worth CA$7,500 a year, so negotiate rates before debating platforms.

Taxes: GST/QST in Québec and VAT OSS in Europe

Platforms can calculate tax at checkout, but registering, collecting and remitting remain your responsibility. At a high level, for a Canadian store: the GST is 5% and the Québec QST is 9.975%. According to Revenu Québec, you are a small supplier, not required to register, while your worldwide taxable supplies stay at or under CA$30,000 in a calendar quarter and over the four preceding quarters.

Businesses outside Canada that sell to consumers in Québec must register for the QST under the specified system once those taxable supplies exceed CA$30,000 over a 12-month period, according to Revenu Québec.

In the European Union, the Your Europe portal states that a VAT threshold of EUR 10,000 applies to distance sales to EU customers; above it, VAT is generally due in the buyer's country. The One Stop Shop lets a business register once and file one return for those sales, and non-EU businesses can use it. The Import One Stop Shop covers low-value imported goods up to EUR 150 per order.

General information, not tax advice. Have an accountant confirm your registrations before you launch in a new market.

Payments in CAD, USD and EUR

Selling in several currencies is mostly a question of conversion fees and payout accounts. Shopify charges a currency conversion fee when you accept payment in a currency different from your payout currency: 1.5% for US stores and 2% in other regions, according to its Help Center. Stripe and WooPayments add similar fees, so the cheapest setup is usually to hold a payout account in each currency you sell in, when your provider supports it.

Rates from Shopify, Stripe and WooCommerce public pricing pages and the Shopify Help Center, viewed September 2026. Premium and business cards may cost more.

When Shopify wins, and a decision table

Shopify wins whenever your catalogue, checkout and fulfilment look like a standard retail store, which is most of the time. It wins on time to launch, on security and uptime you do not manage, and, in our arithmetic, on three-year cost at all three revenue levels. Choose custom for capability, not for savings.

Frequently asked questions

Related

Sources

• Shopify — Pricing, Canada (viewed September 28, 2026)
• Commerce-UI — Shopify Pricing (2026): Plans, Fees and Real Cost Breakdown (2026)
• Shopify Help Center — Fees and costs for international selling
• Shopify Dev — Hydrogen and Oxygen fundamentals
• Eightx — Average Shopify app spend by revenue band, 2026 (June 1, 2026)
• WooCommerce — Pricing (viewed September 2026)
• WooCommerce — WooPayments fees (viewed September 2026)
• Stripe — Pricing, Canada (viewed September 2026)
• Stripe — Pricing, France (viewed September 2026)
• Clutch — E-Commerce Website Development Pricing Guide (updated September 21, 2026)
• HTTP Archive — Technology Report, Core Web Vitals by technology (CrUX, August 2026)
• Revenu Québec — Details concerning small suppliers
• Revenu Québec — Calculating the taxes
• Revenu Québec — Registration under the specified system, suppliers outside Canada
• Your Europe — Cross-border VAT rates in Europe
• Your Europe — EU VAT One Stop Shop (OSS)
• Bank of Canada — Daily exchange rates (September 28, 2026)

Market ranges compiled on September 28, 2026. They are not a ZeniTech quote.