E-commerce Platforms Compared: Shopify vs WooCommerce vs Custom (Kenya)

For most Kenyan businesses starting out, Shopify is the fastest way to a reliable store, WooCommerce is the most flexible if you already run WordPress and want control, and a custom build only makes sense once your operation is complex enough that the platforms start fighting you. Choose based on where your business actually is today, not where you imagine it in five years.

That is the short version. Below is the honest comparison, including where each option quietly costs you, so you buy the right thing once instead of migrating in a panic later. This is the same neutral advice we give in e-commerce and payment integrations work.

The three options in one line each

• Shopify — you rent a polished, hosted store. Fast, reliable, low maintenance, monthly fee plus transaction costs.
• WooCommerce — a free plugin on top of WordPress. Flexible and you own it, but you manage hosting, security, and updates.
• Custom — a store built around your exact workflow. Total control and no per-sale platform tax, but higher upfront cost and real ownership responsibility.

None is "best." Each is best *for a specific situation*.

Shopify: advantages and disadvantages

Advantages: fastest to launch, hosted and secure by default, reliable checkout, huge app ecosystem, good mobile experience out of the box, minimal technical maintenance.

Disadvantages: monthly subscription plus transaction fees that grow with sales, less control over deep customisation, you are renting (limited true ownership), and app costs stack up. M-PESA works but usually through third-party apps rather than natively.

Best for: businesses that want to sell now, value reliability over control, and would rather pay a predictable fee than manage infrastructure. Full breakdown in Shopify in Kenya: pros, cons, and when it fits.

WooCommerce: advantages and disadvantages

Advantages: free core, enormous flexibility, you own the store and data, deep customisation, and strong SEO because it sits on WordPress. Easier to integrate local payments like M-PESA directly.

Disadvantages: you are responsible for hosting, security, backups, and updates. It can become slow or fragile if poorly maintained, and "free" becomes real cost once you add quality hosting, plugins, and maintenance.

Best for: businesses that already publish content on WordPress, want ownership and flexibility, and have a maintenance plan (or a partner). Full breakdown in WooCommerce in Kenya: pros, cons, and when it fits.

Custom e-commerce: advantages and disadvantages

Advantages: fits your exact workflow, no per-sale platform tax, complete control of experience and data, and clean integration with your other systems, inventory, accounting, and dispatch.

Disadvantages: highest upfront cost, longer to build, and you own maintenance and security. Overkill for a simple catalogue.

Best for: businesses whose commerce workflow is unusual, high-volume, or tightly tied to operations, where platforms force expensive workarounds. See custom e-commerce: when to build your own store and the wider custom software vs off-the-shelf decision.

The payments reality in Kenya

Whatever platform you choose, payments make or break a Kenyan store, and M-PESA is non-negotiable. The difference between platforms is how cleanly M-PESA and card payments integrate and reconcile. A store that takes money but forces manual reconciliation is only half-built. Read the complete M-PESA integration guide before you commit.

How to choose in five questions

1. Do you need to launch this month? Lean Shopify.
2. Do you already run WordPress and want to own it? Lean WooCommerce.
3. Is your commerce workflow unusual or tied to operations? Consider custom.
4. Who will maintain it? If nobody, avoid self-managed options or budget for a partner.
5. What do fees cost you at your real sales volume? Model Shopify's monthly plus transaction fees against WooCommerce hosting or a custom build over three years.

The most expensive mistake

Choosing on price alone. A "free" WooCommerce store with no maintenance becomes a security liability. A cheap custom build with no reconciliation becomes a finance nightmare. The cost that matters is total cost over three years, including the hidden work of running the thing. This is the same trap covered in how to choose a technology consultancy.

Frequently asked questions

Which is cheapest overall?

It depends on volume. Shopify is cheapest to start but its monthly and transaction fees grow with sales. WooCommerce is cheap to license but costs real money in hosting and maintenance. Custom is most expensive upfront but has no per-sale platform tax. Model your actual sales volume over three years before deciding.

Can I use M-PESA on all three?

Yes, but not equally cleanly. WooCommerce and custom builds integrate M-PESA most directly. Shopify usually relies on third-party apps. In all cases, insist on proper reconciliation, not just a payment button.

Should a small business ever build custom?

Rarely at the start. Custom earns its cost when your workflow is genuinely unusual or tightly tied to operations. Most small catalogues are served better and cheaper by Shopify or WooCommerce until they clearly outgrow them.

Can I move platforms later?

Yes, but migrations cost time, money, and SEO if done carelessly. That is exactly why choosing the right fit now matters. Pick for where the business is today, with a clear view of the next step.

Not sure which fits your business? Tell us what you sell and how you operate and we will recommend the honest option, even if it is the one we don't build.