Best E-commerce Platform in Kenya (2026): Shopify vs WooCommerce vs Custom

For a Kenyan shop, the platform question comes down to one thing nobody outside Kenya optimises for: how cleanly does it take M-Pesa? Everything else — themes, apps, SEO — is broadly solvable on any modern platform. Payment is where the international options get awkward, and where the decision is really made. Here is how the realistic choices compare in 2026.

The short answer

Shopify in Kenya: strong platform, awkward payments

Shopify is genuinely excellent software. The problem for a Kenyan merchant is that Shopify Payments is not available in Kenya, so you use a third-party gateway — and Shopify charges an extra transaction fee on top of the gateway fee when you do. Add a subscription billed in dollars, which moves with the shilling, and the running cost is real.

• Subscription: roughly USD 29–79 a month for the plans most SMEs use — call it KSh 4,000–11,000 monthly, before apps.
• An extra transaction fee for using an external gateway, on top of what the gateway itself charges.
• M-Pesa works through third-party gateways and apps rather than natively — it works, but it is a bolt-on.
• Apps add up fast: a reviews app, a bundles app and a shipping app can quietly double the monthly bill.
• Best-in-class for SEO structure, speed and abandoned-cart recovery out of the box.

Choose Shopify if you sell internationally, ship physical goods at volume, or need the app ecosystem more than you need cheap M-Pesa. For a Nairobi shop selling to Nairobi customers, it is usually the expensive way to solve a problem Kenya already solved.

WooCommerce: cheap to run, yours to maintain

WooCommerce is a WordPress plugin, so the software is free and you pay for hosting. That makes the running cost the lowest of the mainstream options, and M-Pesa integration through the Daraja API is well-trodden ground in Kenya. The trade-off is maintenance: WordPress needs updates, backups and security attention, and a neglected WooCommerce store gets slow and gets hacked.

• Running cost: hosting from about KSh 8,000–25,000 a year for a small store; no platform commission.
• M-Pesa: mature plugins and straightforward Daraja STK-push integration.
• A huge plugin library — and a real risk of plugin bloat slowing the store to a crawl.
• Needs an owner: updates, backups and caching, or performance degrades within months.
• Excellent for content-led shops that also blog for SEO.

Wix, Squarespace and the drag-and-drop builders

Builders are fine for a handful of products and a founder who wants to do it themselves this weekend. They are weaker on M-Pesa, weaker on SEO control, and you hit a ceiling quickly — at which point migrating a catalogue and its URLs is more painful than starting right. Use them to validate an idea, not to build a business you expect to grow.

Custom-built stores: the Kenyan sweet spot

A purpose-built store — modern framework, lightweight CMS, M-Pesa Daraja wired in directly — costs more upfront and nothing per sale. For a shop doing consistent volume that maths flips quickly: a platform taking a percentage of every transaction plus a monthly fee can cost more in a year than the build did.

Our Premium package builds a 50-product store with M-Pesa and card checkout for KSh 70,000, including the first year of domain and hosting — roughly what a year of Shopify plus apps costs before you have sold anything. If you are starting from scratch, our step-by-step guide to launching an online shop in Kenya covers products, delivery and first sales.

The M-Pesa question, answered properly

There are three ways to take M-Pesa on a website, and they are not equivalent:

• Manual paybill or till — the customer pays, then types the confirmation code into a form. Cheapest, but you reconcile by hand and fraud is easy.
• STK push via the Daraja API — the customer taps “Pay”, a prompt appears on their phone, and your site confirms the payment automatically. This is what a real shop should use.
• An aggregator gateway such as Pesapal, Flutterwave or Paystack — one integration gives you M-Pesa plus cards; slightly higher fees, much less setup.

If you take more than a few orders a week, insist on STK push or a proper gateway. Manual code-entry checkouts lose sales at the last step and eat hours in reconciliation — how M-Pesa integration actually works goes deeper on the Daraja side.

What actually decides whether your shop works

After the platform choice, the things that separate stores that sell from stores that just sit there are unglamorous: product photos that are consistent and well lit, delivery cost shown before checkout, a working WhatsApp button for the many Kenyan buyers who want to ask one question first, honest stock levels, and page speed on a phone. Platform choice sets your ceiling; those five things decide whether you get near it.

Not sure which fits your catalogue and volume? Tell us what you sell and roughly how many orders a month, and we will tell you honestly which of these to build on — including when Shopify is the right answer.