Shopify vs. Amazon: An In-Depth Comparison

Christine GerzonLast Updated: January 25, 2026

0 6 minutes read

Shopify and Amazon remain two of the most powerful forces in e-commerce, but comparing them in 2026 requires a different lens than it did a few years ago. This is no longer just a question of “marketplace vs. website builder.” It’s about control, dependency, distribution, and margins in an environment shaped by AI, rising fees, and off-platform checkout.

Both platforms can work exceptionally well. Both can also quietly box you in if you don’t understand what you’re trading away.

Let’s break it down.

An Overview of Amazon and Shopify

Amazon and Shopify are both designed to solve different problems.

Amazon is a global marketplace. Sellers plug into existing demand, standardized listings, built-in trust, and Amazon’s fulfillment infrastructure. In return, Amazon controls the rules, the customer relationship, and a meaningful slice of your margin.

Screenshot of Shopify plans and pricing landing page.

Shopify is a commerce infrastructure platform. It lets brands build and operate their own storefronts, control their customer data, and design the buying experience end-to-end. Shopify does not provide demand by default. Traffic must be earned, bought, or borrowed.

Which Is Easier to Set Up: Shopify or Amazon?

For speed to first sale, Amazon still wins.

If a product already exists on Amazon, a seller can often start selling in hours by attaching to an existing listing. Design choices are limited, but friction is low.

Shopify requires more upfront work. You’re building a site, choosing a theme, configuring payments, setting up shipping, and thinking about brand presentation from day one. The upside is flexibility. The downside is responsibility.

Where this has changed since 2023 is time-to-scale.

Amazon may get you selling faster, but scaling often introduces:

Category approvals
Brand Registry requirements
Policy enforcement risk
Rising ad dependency

Shopify takes longer to launch but scales with fewer platform-imposed constraints once demand exists.

Amazon vs. Shopify: Pricing (Updated)

Pricing is one of the most misunderstood differences between Shopify and Amazon because the costs behave very differently over time.

Shopify’s fees are typically front-loaded and modular—you pay a monthly platform fee, payment processing, and any apps or services you choose to add. This structure gives sellers flexibility and control, but it also means profitability depends heavily on marketing efficiency and operational discipline.

The platform itself does not take a percentage of your product revenue.

Amazon’s pricing is embedded and variable.

Instead of paying for individual tools, sellers give up a portion of each sale through referral fees, fulfillment costs, and often advertising spend just to remain competitive. While this simplifies operations and speeds up time to market, margins can compress quickly as competition increases or fees change.

At scale, the question is less about which platform is cheaper and more about where you’re willing to absorb cost pressure: upfront in infrastructure or continuously in margin.

Cost Category	Shopify	Amazon
Monthly platform fee	Required. Tiered plans based on features and scale.	Required for Professional sellers.
Per-transaction fees	Payment processing fees apply; additional transaction fees usually waived when using Shopify Payments.	No per-transaction fee, but referral fees apply to every sale.
Referral / commission fees	None. Shopify does not take a cut of product revenue.	Typically around 15% per sale, varies by category.
Fulfillment costs	Optional. Costs depend on 3PL, in-house shipping, or external services.	Required if using FBA. Includes pick, pack, shipping, and returns.
Storage fees	None by default. Storage handled independently.	Ongoing inventory storage fees, higher during peak seasons.
Advertising costs	Optional but often necessary for growth (search, social, influencers).	Increasingly necessary to remain competitive within Amazon search results.
App / tooling costs	Common. Many stores rely on paid apps for subscriptions, bundles, reviews, and analytics.	Limited. Most tools are native or external software subscriptions.
Checkout fees	Flexible. Multiple payment providers supported.	Fixed. Amazon controls checkout and payments.
Margin predictability	Higher. Costs are more controllable and transparent over time.	Lower. Fees, ad costs, and competition can compress margins unexpectedly.

Traffic and Revenue: Amazon vs. Shopify

Amazon still dwarfs Shopify in raw traffic and transaction volume. That hasn’t changed. What has changed is how traffic converts, as AI now plays a direct role in what shoppers see, compare, and ultimately buy.

Amazon traffic comes with built-in advantages that are increasingly reinforced by AI:

High purchase intent from shoppers already primed to buy
Built-in trust tied to Prime, reviews, and Amazon-managed checkout
Algorithmic competition, where visibility is shaped by AI systems such as product ranking models, recommendation engines, and ad optimization tools
AI-powered features like:
- Amazon’s recommendation engine
- Dynamic Buy Box selection
- Automated ad targeting
- Conversational shopping and product comparison tools that help guide shoppers toward purchase-ready listings

On Amazon, discovery is largely automated. Sellers benefit from AI-driven exposure, but visibility is shared, competitive, and constantly recalculated.

Shopify traffic, by contrast, must be earned—but it converts differently when done well, especially with AI tools that support the merchant rather than control the marketplace:

Higher AOV potential, driven by brand storytelling, bundling, and upsells
Better retention, supported by direct customer relationships and remarketing
Full access to customer data, which fuels personalization and long-term value
AI tools such as:
- Shopify Magic
- AI Store Builder
- Shopify Sidekick
- AI-powered search, recommendations, and checkout optimization that help merchants improve conversion once shoppers arrive

Instead of directing traffic, Shopify’s AI enhancements focus on helping brands present products more clearly, reduce friction, and operate more efficiently across marketing, support, and checkout.

The more meaningful question to ask today is no longer “who has more traffic,” but:

Who controls discovery when AI and assistants increasingly mediate shopping?

Marketplaces like Amazon currently hold the advantage in AI-driven discovery, while platforms like Shopify give brands more control over how traffic converts once it arrives.

Customizability of Your Store

Shopify remains the clear winner here.

Themes, apps, checkout customization, bundling, subscriptions, and localization—Shopify allows brands to shape the buying experience in ways Amazon does not.

Amazon offers Brand Stores and A+ Content, but these operate within a fixed framework. Differentiation exists, but it’s constrained.

Amazon optimizes for consistency.
Shopify optimizes for identity.

Order Fulfillment

Amazon FBA remains the gold standard for scale and reliability.

FBA handles:

Storage
Pick, pack, and ship
Returns
Prime eligibility

This convenience comes at a cost, especially for slow-moving or oversized inventory.

Shopify’s fulfillment story has evolved. Rather than positioning a single in-house network as an FBA replacement, most Shopify brands now rely on:

Third-party logistics providers (3PLs)
Hybrid in-house fulfillment
Amazon Multi-Channel Fulfillment (MCF)

MCF allows Shopify brands to use Amazon’s logistics without selling on Amazon, blurring the line between the two ecosystems.

Payment Options

Shopify offers broad payment flexibility:

Shopify Payments
Third-party processors
Local payment methods across regions

This flexibility helps with global expansion but adds complexity.

Amazon abstracts payments almost entirely. Customers trust Amazon’s checkout, and sellers rarely think about conversion mechanics—until fees or account issues arise.

Trust is Amazon’s biggest checkout advantage.
Ownership is Shopify’s.

Seller Autonomy

This is where the philosophical divide becomes operational.

Amazon sellers operate inside Amazon’s rules. Policy enforcement can be sudden, and appeals can be slow. Account risk is real, even for compliant sellers.

Shopify sellers own their storefronts. While Shopify enforces platform rules, store shutdowns are far less common, and brands retain their customer lists, data, and infrastructure.

Shopify Within Amazon: Selling on Amazon as a Shopify Brand

Shopify does not embed its checkout or storefront experience inside Amazon. Instead, it enables merchants to operate Amazon as a sales channel while keeping Shopify as the system of record for products, inventory, and brand operations.

Through native integrations and third-party tools, Shopify merchants can list products on Amazon, sync inventory, and manage orders from their Shopify backend. In this setup, Amazon functions as a demand and fulfillment channel, while Shopify remains the central platform for catalog management, pricing logic, and reporting.

Shopify’s role is largely operational and supportive. Its AI tools help merchants generate product content, manage listings, forecast inventory, and optimize workflows, but they do not influence how products are ranked or discovered on Amazon. Visibility on Amazon is still governed by Amazon’s own algorithms, advertising systems, and marketplace rules.

In practice, this means Shopify brands can use Amazon to access high-intent shoppers while relying on Shopify to maintain consistency across channels. Amazon controls discovery and checkout on its platform, while Shopify provides the infrastructure that keeps multi-channel selling organized and scalable.