WooCommerce vs Shopify: A complete comparison to help you choose the best e-commerce platform in 2025

WooCommerce vs Shopify.

Introduction

As a marketing agency, your main goal is to deliver measurable results for your clients, not to get stuck managing technical platforms or limited customization options.
That’s why one of the most common questions agency owners face before scaling their ecommerce services is:

WooCommerce or Shopify?

Which one is better for agencies that manage multiple online stores and need control, scalability, and operational efficiency?

In this guide, we’ll help you choose the best ecommerce platform for your agency’s model — based on the continuous development experience of WordPress Ongoing and the best practices of leading ecommerce agencies.

Platform Overview

WooCommerce

WooCommerce is an open-source ecommerce plugin for WordPress.
It offers full control over design, functionality, and user experience.
It doesn’t charge transaction fees and can be customized endlessly with over 59,000 plugins and thousands of themes.

For agencies, WooCommerce means technical freedom and unlimited scalability. You can build fully customized stores, integrate them with your marketing stack, and tailor each project to your clients — without platform restrictions.

Want to know more?: Go to the official WooCommerce website.

Shopify

Shopify is a hosted (SaaS) platform designed for simplicity: hosting, security, backups, and support are all included.
In exchange, its closed ecosystem limits customization and adds a monthly fee plus transaction commissions (up to 2% on external gateways).

For agencies that value speed and simplicity, Shopify can be a good fit for MVPs or validation projects, but in the long term it may reduce flexibility and profit margins.

Want to know more?: Go to the official Shopify website.

Quick Comparison Table

Pros and Cons for Marketing Agencies

WooCommerce: Power and Control for Performance-Oriented Agencies

Pros:

• Low entry cost: The plugin is free — you only pay for hosting, domain, and SSL.
• No transaction fees: Full profit margin for the agency or client.
• Deep marketing integration: Advanced SEO, automation, CRM, and tracking options.
• Full customization: Perfect for agencies with development capabilities or technical partners.

Cons:

• Requires ongoing maintenance and technical support (updates, backups, security).
• Costs can increase with premium plugins or high-traffic hosting.

Pro tip: By outsourcing maintenance to a WordPress support partner like WordPress Ongoing, agencies can eliminate the technical burden and focus entirely on scaling.

Shopify: Simplicity and Built-in Support

Pros:

• Instant setup: Launch a store in just hours.
• Zero maintenance: Hosting and updates handled by Shopify.
• Pre-designed themes and visual builder for rapid deployment.

Cons:

• Transaction fees: Up to 2% if you use external gateways.
• Limited flexibility: You can’t modify the core code or add custom features outside its ecosystem.
• Hidden costs: Apps and premium plans can significantly raise the total cost of ownership (TCO).

Key Considerations Before Choosing

1. Evaluate Your Agency Model

If your agency offers ongoing maintenance or development services, WooCommerce fits better — it enables recurring revenue through support, optimization, and SEO retainers.
If your business focuses on fast delivery projects or MVPs, Shopify can be faster to validate.

2. Define Your Level of Control

• WooCommerce = Absolute control + innovation freedom.
• Shopify = Less control, but greater simplicity and managed stability.

3. Assess Your Marketing Ecosystem

WooCommerce integrates seamlessly with any marketing, automation, or CRM tool, allowing full data connectivity across projects.
Shopify, while robust, limits certain integrations or requires paid apps.

4. Calculate the Total Cost of Ownership (TCO)

For agencies, TCO matters more than upfront price.
WooCommerce tends to be more cost-effective long-term — especially if you manage multiple clients under a shared maintenance and hosting infrastructure.

Conclusion: The Hybrid Strategy Used by Leading Agencies

Top-performing agencies often use a hybrid approach:

• Shopify for fast-launch projects and market testing.
• WooCommerce for scalable, high-performance stores with complete branding and marketing control.

If your goal is to scale your services without worrying about technical support, WordPress Ongoing can become your technical partner — letting you focus on strategy, growth, and client relationships.

Outsource your WordPress support and deliver secure, fast, and scalable ecommerce solutions — without increasing your workload.

If your agency manages multiple WordPress projects and you want to scale without worrying about technical support, check out our Complete Guide for Marketing Agencies.