Shopify vs Custom Ecommerce: The Real Cost After Year Two

The Shopify vs custom ecommerce debate often starts with the claim that the platform takes a cut of every sale. For stores that use Shopify Payments, that is not quite right. You pay card processing on any store, custom or not, and Shopify's rates are competitive. The real differences sit elsewhere: the plan, the apps and the theme work on one side, and the cost of building and running your own store on the other.

Year two is the useful moment to compare. By then a custom store's build cost has been paid, and only the running costs decide which route is cheaper from there on.

What Shopify charges, as of October 2026

The card rates are Shopify's standard online rates for domestic cards through Shopify Payments. The extra fee in the last column applies only when a store uses a third-party payment provider instead. Apps are priced separately by their developers, and many bill monthly.

For comparison, Stripe's standard US pricing is 2.9% + 30¢ per successful domestic card transaction, plus 1.5% for international cards and 1% when currency conversion is needed. A custom store on Stripe therefore pays about what Shopify Basic pays per order, and a little more than Grow or Advanced, until its volume justifies negotiating custom pricing.

The costs that grow after year one

• Apps. Reviews, subscriptions, upsells, bundles, search and loyalty programs each arrive as a separate monthly bill, and the list is easier to grow than to shrink.
• Sales tax. Shopify Tax is free until a store reaches $100,000 in annual sales. After that, US stores on Basic, Grow or Advanced pay 0.35% on orders where tax is calculated, capped at $0.99 an order and $5,000 a year per region. A custom store pays too: Stripe Tax's basic plan charges 0.5% per transaction where you are registered to collect, or $0.50 per transaction through its API.
• Theme and design work. New sections, redesigns and fixes when apps conflict with each other.
• Running your own. A custom store needs hosting, security updates, monitoring and developer time for changes. Stripe's integration guide also notes that any business accepting cards must do so in a PCI-compliant manner and attest to that every year; hosted payment fields keep that burden small.
• The move itself. Switching is a one-time cost of its own: exporting data, mapping redirects, testing checkout and running both stores side by side for a short period.

A worked example

Take an illustrative store selling $20,000 a month online with an $80 average order: 250 orders a month and 3,000 a year, all on domestic cards and all with sales tax calculated. The two lines marked as assumptions stand in for your own invoices.

The arithmetic: 12 × $79 for the plan; 2.7% or 2.9% of $240,000, plus 3,000 × 30¢, for processing; 0.35% of the $140,000 above Shopify's free threshold, or 0.5% of all sales on Stripe, for tax. On these assumptions the running costs are almost identical, and Shopify is cheaper before the custom build is even counted. A custom build would never pay for itself here. A store with many overseas customers would widen the gap, since Shopify adds 1% for international cards and Stripe adds 1.5%.

Now change one line. If the store's apps cost $600 a month instead of $150, Shopify's total rises to $16,018 a year and the custom store saves $5,158 a year. A custom build costing $10,000 more than a Shopify setup would then pay for itself in about two years. Count only the apps whose jobs a custom build will truly take over; email marketing, review platforms and subscription billing often remain paid services on a custom store too.

The general test: divide the extra cost of the custom build by the yearly running cost it saves. If the saving is small or negative, stay on Shopify. Our look at the five-year math of owning versus renting software applies the same logic to a whole software stack.

When a custom store is the better buy

• Your app bill is large and growing, and a build can replace what those apps do.
• Your sales model fights the platform: quotes and approvals, trade pricing, product configurators, rentals, or bookings sold alongside products.
• You face Plus-level pricing of $2,300 a month or more, with needs specific enough that a bigger plan still will not meet them.
• You need checkout and order data inside your own systems, such as an ERP or a custom fulfillment process.

When Shopify is the right answer

• You are new or unproven. Shopify Basic is faster to launch and cheaper to walk away from if the product does not sell.
• Your catalog and checkout are standard. If a theme and a few apps do the job, a custom build buys little.
• Your app spending is modest. As the example shows, the running costs then barely differ.
• Nobody will maintain the code. A custom store needs updates, monitoring and a yearly PCI attestation. Without a maintenance plan, stay on a platform that handles those for you.

Questions to settle before you switch

1. What did the store cost over the last 12 months, line by line: plan, apps, tax fees and any third-party transaction fees?
2. Which apps would a custom build replace, and which would stay as paid services?
3. What card rates can you get at your volume, from Stripe or another processor?
4. How will products, customers, orders and URLs move, and who maps the redirects that protect your search rankings?
5. Who maintains the code, and what does that cost each month?
6. Will the code, domain, payment accounts and customer data all be in your name?

Where OWNIT fits

OWNIT builds owned online stores from $4,000, connected to the client's own Stripe account or preferred processor, with checkout, inventory, customer accounts, abandoned-cart flows, shipping rates and tax calculation wired in from the start. Physical products, digital downloads, memberships and subscriptions are all supported, and most stores launch in a few weeks depending on catalog size. OWNIT also migrates products, customers, orders and SEO from Shopify or WooCommerce. If the numbers say Shopify is the better fit for your store, we will tell you on the call. The e-commerce service page shows store demos and how a migration runs.