For most companies, Shopify is the better starting point, and custom ecommerce makes sense only when a core buying workflow cannot run on it. That usually means complex pricing, configured products or regulated selling. Here is how we help buyers test the decision, using current fees and plan limits.
When is Shopify the better choice?
Shopify usually wins when your store works like most stores: a catalog, a cart, standard promotions, and shipping and tax rules that apps can handle. You get hosting, checkout and a large app ecosystem without running them yourself.
It is also a strong fit when speed matters more than uniqueness. If the goal is to test a direct channel or sell a merchandise line, building a custom platform first usually means spending months on parts customers will never notice.
Size alone does not rule Shopify out. Shopify now allows 2,048 variants per product, up from the old limit of 100, and its Plus plan supports 9 expansion stores. Those two changes remove objections we used to hear from larger catalogs and multi-brand teams.
When does custom ecommerce make sense?
Custom work earns its cost when the buying process itself is the product or the advantage. These are the situations we look for:
- Complex pricing. Prices depend on contracts, configurations, live quotes or rules that change by customer.
- Configured products. Buyers design or specify the item, and the order drives production.
- Regulated selling. Eligibility checks, licenses or approvals have to happen before purchase.
- Deep operational ties. The store has to work closely with an ERP, a warehouse system or a field team.
Notice what is not on the list: wanting a distinctive design. Most design needs can be met with a custom Shopify theme. Our custom development team starts by asking which workflow a platform cannot handle, because that answer decides most of the budget.
What does Shopify really cost as you grow?
Compare the full cost, not just the plan price. Shopify lists these monthly prices in the US at the time of writing, along with the extra fee for using an outside payment provider:
- Basic: $39 paid monthly, or $29 paid yearly. Third-party fee: 2%.
- Grow: $105 paid monthly, or $79 paid yearly. Third-party fee: 1%.
- Advanced: $399 paid monthly, or $299 paid yearly. Third-party fee: 0.6%.
- Plus: starts at $2,300 a month. Third-party fee: 0.2%.
That fee is where the math often changes. Shopify says these fees apply to all transactions processed through third-party gateways, even when Shopify Payments is active, with an exemption for PayPal if Shopify Payments is your primary provider. On $1 million processed through an outside gateway, the fee is $10,000 on Grow and $2,000 on Plus, before your provider's own charges.
Then add the costs that do not appear on the pricing page: paid apps, theme work, and the staff time spent keeping them working together. Check current prices before you decide, since they can change and differ by country.
What are the checkout and B2B limits?
Test these before you commit, because they are the limits most likely to force an upgrade or a rebuild.
Checkout customization is presented as a Plus capability, so a lower plan may not give you the checkout you are picturing. If your plan depends on changing checkout logic, price Plus into your comparison from the start.
B2B is more available than many teams assume. Shopify says B2B is available on all plans, and companies, net terms, quantity rules and draft orders are included. The gaps appear with more complex accounts:
- Basic, Grow and Advanced allow 3 active catalog assignments across active B2B markets. Plus is unlimited.
- Catalogs assigned directly to a company or location are Plus only.
- Deposit requirements and partial payments are Plus only.
If every large customer has its own negotiated price list, those limits matter a great deal. If you have three price tiers, they may not matter at all.
How do integrations change the decision?
For most companies, the hard part is not the storefront. It is keeping inventory, orders, customers and accounting correct across systems. That work exists on either path.
Before choosing, write down each system the store has to talk to, which one owns each piece of data, and how fresh that data must be. Then decide what happens when a sync fails, such as an order that never reaches the warehouse. Our guide to ecommerce API integration covers this in more depth.
A middle path often works: keep Shopify for the catalog and checkout, and build custom services for pricing, configuration or fulfillment logic. Teams may also use Shopify's commerce engine with a separately built front end, known as headless. That gives you more control, but you take on a front end to host and maintain, so we suggest it only when you can name what the standard theme stops you from doing.
What does custom add after launch?
A custom store means you own its running costs for as long as it exists. Budget for hosting, monitoring, security patches, tax and payment changes, accessibility fixes and a team who knows the code.
Security deserves its own line. Handling accounts, orders and checkout yourself means your team owns more of that risk. Our ecommerce security guide lists what to check. If a vendor quotes only the build and says nothing about the following years, the quote is incomplete.
How should you make the call?
- List your must-have workflows. Write the five to eight buying scenarios that have to work, including the awkward ones like returns and contract pricing.
- Test them in a Shopify trial. Mark each as native, solved by an app, or needing custom work.
- Compare multi-year cost. Include plan, fees, apps and staff time on one side, and build, hosting and maintenance on the other.
- Plan your exit. Confirm you can export products, customers and orders, on either path.
- Pick the smallest path that passes. Start with Shopify if it handles your scenarios, then add custom services only where it falls short.
Frequently asked questions
It can be. Plus adds expansion stores, checkout customization and deeper B2B features. The test is whether your specific pricing, checkout and integration needs fit, not your revenue.
Yes, for many cases. Shopify offers B2B on all plans, with companies, net terms and quantity rules. Direct company catalogs, deposits and partial payments are Plus only, so complex accounts should check those limits.
It depends on workflows, integrations and compliance needs, so a single figure would mislead you. Get quotes based on your written scenarios, and ask each vendor to include hosting and maintenance over several years.
Yes, and starting on Shopify is often a sensible way to learn what customers actually need. Keep your product, customer and order data exportable, and plan redirects so you protect search traffic during the move.
Sources
- Shopify: Pricing
- Shopify Help Center: Third-party payment providers
- Shopify Help Center: Shopify Plus plan
- Shopify Help Center: B2B plan features
- Shopify developer changelog: Product variant limit is now 2,048 (October 15, 2025)
Deciding between Shopify and a custom build?
We can walk through your buying scenarios, mark what fits the platform, and scope only the custom work you actually need.
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