Shopify vs Amazon (2026): Your Own Store, the Marketplace, or Both?

Shopify and Amazon aren't really the same kind of product. Amazon is a marketplace: you list products in front of shoppers who are already there, and Amazon controls the storefront, the checkout and the customer relationship. Shopify is the software for running your own store: you control the brand, the site and the customer data, but you have to bring the traffic.

So the useful question isn't "which is better" but "what role should each play." As of October 2026, most brands that can build demand are better off with a Shopify store as the home base, using Amazon as an additional channel for reach. Brands selling commodity or search-driven products, where shoppers start on Amazon, may get most of their sales there and use a Shopify store mainly for brand building and repeat customers.

This guide compares fees from Amazon's and Shopify's own pricing pages, explains who owns the customer on each, and shows how to run both from one Shopify admin. More Shopify guides are in our Shopify hub.

How each model works

Amazon gives you access to an existing audience. You list products in Amazon's catalog, compete for placement in Amazon search, and choose whether Amazon fulfills orders through Fulfillment by Amazon (FBA) or you ship them yourself. Brand owners can enroll in Amazon Brand Registry for tools like a Brand Store, enhanced product pages and Brand Analytics.

Shopify gives you a store under your own domain, your own checkout (with Shop Pay and other wallets), your own email and SMS marketing, and full control over pricing, bundles, subscriptions and design. Traffic comes from search, ads, social, email and, increasingly, AI channels such as ChatGPT and Google AI Mode through Shopify's Agentic Storefronts.

Fees compared

Amazon's seller pricing page splits fees into selling plan fees and referral fees. Shopify's are on shopify.com/pricing.

Amazon referral fee examples

From Amazon's US pricing page on 1 Oct 2026:

Media items (books, DVDs, music, software, video) also carry a $1.80 closing fee per item. Amazon notes that a product's fee category "may not be the same as the category that appears to customers." Amazon also advertises incentives for new-to-Amazon brands, including referral-fee waivers in the first year, so check current terms when you start.

A worked example

Take a $40 home and kitchen product, before fulfillment, ads and product cost:

• Amazon (Professional): 15% referral fee = $6.00 per unit, plus $39.99 a month for the plan.
• Shopify (Basic, Shopify Payments): 2.9% + 30¢ = $1.46 per order, plus $39 a month billed monthly.

Shopify keeps about $4.54 more per order, but that's only half the story. On Amazon, the $6.00 buys access to shoppers who were already searching. On Shopify, you need to spend on ads, content or email to get the same visitor, and that customer acquisition cost often exceeds the fee difference for a new brand. The math flips for repeat customers: a second order on your own store costs only processing, while every repeat order on Amazon pays the full referral fee again.

Who owns the customer

This is the biggest structural difference. Amazon's Seller Code of Conduct says:

• "All communications to customers must be sent through Buyer-Seller Messaging and be necessary for fulfilling the order or providing customer services. Marketing communications are prohibited."
• Customer details received to fulfill orders may be used "only to fulfill orders" and must be deleted "after the order has been processed."
• Sellers "may not provide links or messages that prompt users to visit any external website or complete a transaction elsewhere."

In practice, an Amazon sale doesn't give you a customer you can market to. On Shopify, the customer record, email consent and order history sit in your admin. You can run email, SMS and WhatsApp campaigns through Shopify Messaging or tools like Klaviyo, build loyalty programs and segment customers by behavior. That's what makes lifetime value and retention marketing possible.

Brand control and pricing

On Amazon, your product page follows Amazon's detail-page format and policies, and you compete with other listings in the same search results. Brand Registry adds brand-building tools and protection benefits, but Amazon still controls the experience and the rules.

On Shopify, you control design, product storytelling, bundles, subscriptions, gift-with-purchase offers, loyalty pricing and the checkout experience (within Shopify's checkout framework). That freedom matters most for premium, giftable or story-driven products, and less for commodity items where price and delivery speed win.

Running both from Shopify

Most growing brands don't choose; they use Shopify as the system of record and add Amazon as a channel.

• Marketplace Connect: Shopify's legacy Amazon sales channel app is no longer available. Its replacement, Shopify Marketplace Connect, says "Sell on Amazon, Target Plus, Walmart, and eBay from Shopify," so you can manage those marketplaces from your Shopify admin. Shopify's pricing page lists it as free for 50 synced marketplace orders a month, then 1% up to $99 a month.
• Amazon fulfillment for your own store: the "Amazon MCF and Buy with Prime" app lets Amazon fulfill your Shopify orders (Multi-Channel Fulfillment) and, in the US, show a Prime-branded checkout option through Buy with Prime.
• One inventory pool: keeping stock in Shopify and syncing out reduces overselling across channels.

Before syncing, check that your product data meets Amazon's listing requirements for your category, because a clean Shopify catalog doesn't automatically satisfy another marketplace's rules. Our guide to Shopify shipping and fulfillment covers the fulfillment side.

Which approach fits your business?

Lean on Amazon when

• Shoppers in your category start their search on Amazon and buy on price and delivery speed.
• You're testing demand and don't yet have budget for paid acquisition.
• You want FBA to handle storage, shipping and returns.

Build on Shopify when

• Your brand, story or product range justifies a direct relationship with customers.
• Repeat purchase, subscriptions or loyalty drive your margins.
• You want control over pricing, bundles, content and data.

Do both when

• You have demand on Amazon and want to convert some of it into direct, repeat customers over time (within Amazon's rules, which prohibit diverting Amazon customers).

If you've built on Amazon and want your own store as the primary channel, see our Amazon to Shopify migration guide.

Conclusion

Amazon trades a commission on every sale for instant access to demand, and it keeps the customer relationship. Shopify trades a monthly plan and your own marketing spend for ownership of the brand, the data and repeat revenue. For most brands, the strongest setup is a Shopify store as the home base with Amazon connected as a channel. eSEOspace helps brands grow that home base with Shopify SEO services.

Frequently asked questions