Everyone says "just use Shopify." It's fast, easy, and looks cheap at first glance. But after three to five years of real-volume operation, the numbers start to shift — and businesses discover they have been paying more than they would have with a custom solution. This article breaks down the true cost of both paths, without the marketing spin.
Shopify: What You Actually Pay
Shopify presents pricing as clean monthly tiers. The reality is more layered.
Subscription Tiers
The base plans look like this:
| Plan | Monthly Price (annual billing) | Staff Accounts |
|---|---|---|
| Basic | $29/mo | 2 |
| Shopify | $79/mo | 5 |
| Advanced | $299/mo | 15 |
| Plus | from $2,300/mo | Unlimited |
For most mid-sized stores, this realistically means the Shopify or Advanced plan — $79–$299 per month.
Transaction Fees — The Biggest Hidden Cost
If you are not using Shopify Payments (available in some markets but with limitations), you pay a platform transaction fee on top of your payment gateway fees:
- Basic: 2% per transaction
- Shopify: 1% per transaction
- Advanced: 0.5% per transaction
That sounds small. On $200,000 annual revenue at the Shopify plan, that is $2,000 per year in platform transaction fees alone — before your payment gateway takes its cut (typically another 1.5–3%).
Practical tip: When evaluating plans, always calculate the total transaction cost: Shopify fee plus payment gateway fee. On $400,000 annual revenue, the difference between plans can be thousands of dollars per year.
Apps and Extensions
Base Shopify is surprisingly limited. Advanced product filtering, automated email flows, loyalty programs, B2B functionality, detailed analytics, accounting integrations — all of these require paid apps. Typical app costs for a mid-sized store:
| App Category | Monthly Cost |
|---|---|
| Advanced search / filters | $15–$80 |
| Email marketing | $20–$150 |
| Product reviews | $10–$50 |
| Subscriptions / recurring billing | $49–$299 |
| B2B and wholesale | $50–$500 |
| Translation and localization | $20–$100 |
Real monthly app costs for a mid-sized store typically land between $100 and $500 per month.
Theme and Design
Premium Shopify themes cost $200–$350 as a one-time purchase. Customization is limited — Shopify does not let you touch the checkout or the core page structure. If you want a unique checkout flow or non-standard layout, you hit a wall. Professional theme customization adds another $800–$3,500 on top.
Custom E-shop: Real Numbers
A custom e-shop — built on WooCommerce, Shopware, Medusa.js, or a fully bespoke solution — has a different cost profile.
Initial Investment
| Solution Type | Approximate Cost |
|---|---|
| WooCommerce + premium theme + basic customization | $1,200–$3,200 |
| WooCommerce / Shopware with significant customization | $3,200–$8,000 |
| Fully custom solution | $8,000–$24,000 |
The relevant comparison category for most growing businesses is $3,200–$8,000: a store with custom design, ERP or accounting integration, advanced filters, and specific business logic.
Ongoing Costs
A custom e-shop does not charge platform transaction fees. You pay only:
- Hosting: $20–$120/month (VPS or managed hosting)
- SSL, domain, monitoring: $5–$15/month
- Payment gateway: 1.5–2.5% of transaction value (to the bank only, not the platform)
- Maintenance and updates: $80–$400/month depending on your agreement
When Shopify Stops Being Cheaper
Here are the numbers for a store doing $200,000 annual revenue:
| Cost | Shopify Advanced | Custom E-shop |
|---|---|---|
| Platform / hosting | $3,600/yr | $720/yr |
| Platform transaction fee | $1,000/yr (0.5%) | $0 |
| Payment gateway | $3,000–$5,000/yr | $3,000–$5,000/yr |
| Apps / extensions | $1,200–$2,400/yr | $0–$800/yr |
| Maintenance | Included | $960–$2,400/yr |
| Total annual operating cost | ~$8,800–$12,000 | ~$4,700–$8,900 |
At $200,000 annual revenue, a custom solution can save $3,000–$5,000 per year. At $400,000 in annual revenue, the savings are even more pronounced — because transaction fees scale linearly with volume.
Real-world example: Hartmann Outdoor, a mid-sized Czech outdoor gear retailer, was running on Shopify's Shopify plan with approximately $320,000 in annual revenue. Between transaction fees and apps, they were paying over $6,000 per year to the platform ecosystem. After migrating to a custom WooCommerce solution (total investment $4,800, hosting and maintenance $140/month), their annual operating costs dropped by $3,200. Payback period: under 18 months.
What Shopify Actually Limits You On
Shopify is a well-designed platform — for standard use cases. The moment you deviate from the standard, you start hitting walls.
Checkout is a closed black box. On plans below Plus, you cannot meaningfully customize the checkout. Complex discount logic, upsells inside checkout, specific payment terms for B2B customers — these either do not work or require expensive Shopify Plus.
Your data lives in Shopify, not with you. Data exports are limited and the format is not always compatible with what you need elsewhere. If you decide to leave, data migration is a painful process.
API integrations have limits. The Shopify API has rate limits and does not always allow the integration depth you need. Connecting a specific ERP or custom warehouse management system usually means compromises.
Multi-language and multi-currency sales are awkward. Shopify Markets is better than nothing, but managing content across multiple languages remains cumbersome.
Practical tip: Before committing to Shopify, list every feature you will need in the next 2–3 years. Apply this rule: if more than 3 key features require paid apps or a Shopify Plus upgrade, recalculate total costs against a custom build.
What a Custom E-shop Gives You
A custom solution is not just about avoiding fees:
No middleman between you and the customer. You pay only the payment gateway. The checkout is yours — you can modify it, A/B test it, personalize it.
Unrestricted integrations. Connect to your ERP, WMS, PIM, or BI tools without the compromises imposed by Shopify's API limits.
You own the data. The full database, all customer records, complete analytics data — you access it, not the platform.
Unique UX. Shopify stores look like Shopify stores. A custom solution looks exactly the way you want — and differentiates you from competitors.
Scaling without penalty. Revenue grows, platform costs do not scale with it. Growing business needs do not automatically mean a more expensive tier or a new app subscription.
Who Should Use Shopify
Shopify makes sense for specific profiles:
- You are starting out and testing the market. Shopify enables a fast launch without significant upfront investment. Before you know e-commerce will sustain your business, it is a sensible choice.
- You sell standard products with straightforward rules. Typical B2C products, no complex pricing for different customer groups, no complicated stock management.
- Annual revenue under $120,000. Below this threshold, platform and transaction costs on Shopify generally do not exceed the total cost of ownership for a custom solution.
- You have no technical team. Shopify does not require developers for day-to-day operations.
Who Should Build Custom
A custom e-shop is the right call when:
- Revenue exceeds $200,000 per year and transaction fees have become a meaningful line item.
- You have specific integration requirements — a proprietary ERP, a custom warehouse system, B2B pricing tiers.
- You need a non-standard checkout — multi-step purchase flows, custom payment logic, subscription billing you can design yourself.
- Brand differentiation matters and you do not want to look like every other Shopify store.
- You are planning international expansion with multiple languages, currencies, and local payment methods.
Five-Year Cost Comparison
For a store doing $320,000 annual revenue with standard integration needs:
| Shopify Advanced | Custom E-shop (WooCommerce) | |
|---|---|---|
| Initial investment | ~$1,000 (theme + setup) | ~$4,800–$7,200 |
| Annual operating costs | ~$9,600–$12,800 | ~$3,200–$5,600 |
| Five-year total | ~$49,000–$65,000 | ~$20,800–$35,200 |
| Code and data ownership | No | Yes |
| Flexibility | Limited | Full |
Over a five-year horizon, a custom solution can save $16,000–$30,000 — on operating costs alone, before accounting for the value of full flexibility and data ownership.
Real-world example: A Czech wholesale textile company was doing around $480,000 in annual revenue through Shopify and paying over $9,000 per year to the platform ecosystem. A custom WooCommerce solution with warehouse system integration cost $7,800 upfront and brought annual operating costs down to $3,600. The saved money went into paid campaigns. The investment paid for itself within 16 months.
A Quick Decision Framework
Answer these questions:
- What is your current or projected annual revenue in 2 years? Under $120,000 — Shopify makes sense. Over $200,000 — recalculate custom.
- Do you need a non-standard checkout or pricing logic? Yes — custom solution.
- Do you have or plan specific integrations (ERP, WMS)? Yes — custom solution or Shopify Plus (expensive).
- Does unique design and UX matter to your brand? Yes — custom solution.
- Do you need to launch in under 4 weeks and just test the market? Yes — Shopify makes sense.
At BASAD Studios, we build e-shops to fit your actual business — from WooCommerce setups with ERP integrations to fully bespoke platforms built for specific workflows. If you want to work out which path costs less over your planning horizon, get in touch or check out our e-shop services.