E-commerce in 2025 is booming. Businesses in Nigeria and across the globe are shifting online, and the demand for professional, scalable e-commerce websites has never been higher. But one big question remains: how much does it cost to build and run an e-commerce website in 2025?

From Shopify, the all-in-one platform, to WooCommerce, the flexible open-source solution, to custom-built e-commerce platforms, the cost differences are significant. Choosing the right one depends on your budget, goals, and long-term vision.

In this detailed breakdown, we will compare Shopify vs WooCommerce vs Custom Build in 2025, using Nigerian Naira (₦) for cost estimates, so you can decide which option is best for your business.

1. What Determines the Cost of an E-commerce Website?

Before diving into each option, let’s outline the main factors that affect your e-commerce costs:

• Platform fees – Monthly subscriptions (Shopify), one-time license, or development costs.

• Hosting & domain – Included on Shopify, but separate for WooCommerce and custom builds.

• Design & themes – Free or premium templates vs custom UX/UI design.

• Plugins & apps – Paid extensions for payments, shipping, SEO, and marketing.

• Payment gateway charges – Typically a percentage of every transaction.

• Maintenance & updates – Ongoing technical support and bug fixes.

• Marketing & SEO – Paid ads, email campaigns, and search optimization.

Now let’s break down each option.

2. Shopify: All-in-One, Scalable, but With Hidden Costs

Shopify Pricing in 2025 (Naira Conversion)

• Basic Plan: $29 ≈ ₦45,000/month

• Shopify Plan: $79 ≈ ₦123,000/month

• Advanced Plan: $299 ≈ ₦465,000/month

• Shopify Plus (Enterprise): $2,300+ ≈ ₦3,570,000+/month

Conversion at approx. ₦1,550 = $1 (2025 average black market rate). Adjust as needed.

Extra Costs

• Themes: ₦250,000 – ₦400,000 (premium one-time purchase).

• Apps: ₦15,000 – ₦300,000/month (depending on the number of apps).

• Transaction Fees: 2.9% + ₦450 per transaction (Shopify Payments). If you use Paystack or Flutterwave, add 0.5–2% extra charges.

Pros of Shopify

✅ Very easy to set up (no coding).
✅ Hosting, SSL, and security included.
✅ Thousands of apps and integrations.
✅ Excellent uptime and scalability.

Cons of Shopify

❌ Monthly fees increase as you scale.
❌ Apps add hidden recurring costs.
❌ Limited customization compared to WooCommerce or custom builds.

Total Shopify Cost Estimate (Yearly, Small Business)

• Setup (theme + apps): ₦300,000 – ₦700,000

• Ongoing yearly fees: ₦540,000 – ₦1,500,000

• Transaction fees: 2.9% per sale

Best for: Startups, SMEs, and entrepreneurs who want a quick, hassle-free setup.

3. WooCommerce: Flexible and Cost-Effective (But Technical)

WooCommerce Base Costs

• Plugin: Free.

• Domain: ~₦18,000/year.

• Hosting: ₦120,000 – ₦600,000/year (basic shared hosting to managed WordPress hosting).

• SSL Certificate: ₦20,000 – ₦50,000/year (sometimes included).

Add-Ons & Extensions

• Premium theme: ₦100,000 – ₦250,000 (one-time).

• Plugins (subscriptions, SEO, shipping, etc.): ₦50,000 – ₦400,000/year.

• Payment processing (Paystack, Flutterwave, Stripe): ~2.9% + ₦450 per transaction.

Pros of WooCommerce

✅ Total ownership of your store.
✅ Highly customizable with WordPress ecosystem.
✅ No mandatory monthly SaaS fees.
✅ Strong SEO tools (Yoast, Rank Math).

Cons of WooCommerce

❌ Requires technical knowledge (setup, updates, security).
❌ Hosting costs can rise with traffic.
❌ Paid plugins can add up.

Total WooCommerce Cost Estimate (Yearly, Small Business)

• Setup: ₦200,000 – ₦500,000

• Ongoing yearly fees: ₦180,000 – ₦900,000

• Transaction fees: ~2.9% per sale

Best for: Nigerian businesses that want full control, are cost-conscious, and can handle (or hire for) technical work.

4. Custom E-commerce Build: Tailored, but Expensive

Development Costs in Nigeria (2025)

• Basic Custom Store: ₦7,000,000 – ₦15,000,000

• Advanced Mid-Level Store: ₦15,000,000 – ₦35,000,000

• Enterprise Custom Build: ₦50,000,000 – ₦150,000,000+

These costs include UX/UI design, backend development, API integrations, and testing.

Ongoing Costs

• Hosting: ₦500,000 – ₦5,000,000/year (cloud servers like AWS, Azure).

• Maintenance & support: ₦2,000,000 – ₦10,000,000/year (depending on SLA).

• Marketing, SEO, and ads: ₦1,000,000+ monthly for serious scaling.

Pros of Custom Build

✅ Unlimited flexibility and features.
✅ Unique design tailored to brand identity.
✅ Scales seamlessly with large operations.
✅ Strong security and proprietary ownership.

Cons of Custom Build

❌ Very high upfront cost.
❌ Long development timeline (3–12 months).
❌ Requires a skilled tech team for maintenance.

Best for: Banks, fintechs, major retailers, and enterprises with complex requirements.

5. Cost Comparison Table (Shopify vs WooCommerce vs Custom Build)

6. SEO Impact of Each Option (Nigeria 2025)

• Shopify: SEO-friendly but limited URL customization. Needs apps for advanced SEO.

• WooCommerce: Best SEO flexibility with WordPress plugins. Perfect for Nigerian SMEs targeting organic traffic.

• Custom Build: Can be fully SEO-optimized if developers implement best practices, but depends on skill level.

7. Which Option Should You Choose?

• Pick Shopify if you want speed, simplicity, and don’t mind higher recurring fees.

• Pick WooCommerce if you want flexibility, SEO control, and can handle technical maintenance.

• Pick Custom Build if you are a large Nigerian enterprise with unique requirements and deep budgets.

In 2025, the cost of building an e-commerce website in Nigeria ranges from ₦200,000 for a simple WooCommerce setup to ₦150 million+ for an enterprise custom build.

• Shopify is convenient but expensive long term.

• WooCommerce is flexible and cost-effective for SMEs.

• Custom builds are powerful but only practical for enterprises.

Your decision should align with your budget, technical expertise, and growth goals. For most Nigerian SMEs in 2025, WooCommerce offers the best balance of cost and control, while startups prefer Shopify for simplicity, and large companies go custom for scalability.