Amazon vs Shopify (2026): Fees, Margins, Data and How to Sell on Both

Amazon vs Shopify is not really an either/or choice for most ecommerce brands. Amazon is a marketplace: it brings buyers who are already shopping, in exchange for referral fees (15% in most categories), fulfillment fees if you use FBA, and very little ownership of the customer. Shopify is a platform for your own store: you keep the customer data, the brand experience and more of each sale, but you have to bring your own traffic. Most growing brands end up selling on both, using Shopify as the home base and Amazon as a high-intent sales channel. This guide compares the fees, margins, data, traffic and control on each side, explains how to run both together, and finishes with a practical section on Amazon listing optimization.

Amazon vs Shopify at a glance

Fee figures in this guide come from Amazon's sell.amazon.com pricing page and Shopify's own pricing page, checked in October 2026. Both companies change fees regularly, so confirm the numbers for your category and country before building a forecast.

What selling on Amazon actually costs

Amazon's fees stack. Most sellers pay three layers: an account fee, a referral fee on every sale, and fulfillment and storage fees if they use Fulfillment by Amazon.

Selling plan fees

• Individual plan: $0.99 per item sold, no monthly fee. Suits testing a handful of products.
• Professional plan: $39.99 per month plus selling fees. This is the plan any serious brand uses, because it unlocks advertising, bulk listing tools and other features.

Referral fees

Amazon takes a referral fee on every item sold, calculated as a percentage of the total sale price. Per Amazon's pricing page, rates range from 3% to 45% depending on category, and 15% is the most common rate (it applies to categories like Home and Kitchen, Toys and Games, Sports and Outdoors, Office Products and "Everything Else"). Most categories also have a $0.30 minimum per item, and you pay whichever is greater. Media items (books, music, video, DVDs, software) carry an extra $1.80 closing fee.

FBA fees

If you use Fulfillment by Amazon, you also pay a per-unit fulfillment fee based on the product's size tier and shipping weight, plus monthly storage fees based on the cubic volume of inventory you keep in Amazon's warehouses. Amazon also charges various inventory-related fees and seasonal peak fees, and these change at least once a year. Rather than quote rates that may already be out of date, the reliable approach is to run each SKU through Amazon's FBA Revenue Calculator and check the Fee Preview report in Seller Central.

What selling on Shopify actually costs

Shopify charges a monthly subscription and payment processing, and that is the bulk of the platform cost. The plans are Basic, Grow, Advanced and Plus. Plan prices and card rates vary by country, so check shopify.com/pricing for your market; in the US, Shopify lists Basic, Grow and Advanced as monthly plans with a discount for annual billing, and Plus as a custom-priced enterprise plan.

• Payment processing. With Shopify Payments you pay a card rate per transaction that gets lower on higher plans.
• Third-party payment providers. If you use another processor instead of Shopify Payments, Shopify adds its own transaction fee: 2% on Basic, 1% on Grow, 0.6% on Advanced and 0.2% on Plus, per Shopify's pricing page.
• Apps and theme. Most stores pay for some apps and possibly a premium theme. These vary widely by store.
• Traffic. This is the real cost. Shopify gives you no shoppers. Paid ads, content, SEO, email and creators all cost money or time.

For a fuller breakdown of build and running costs, see our guide to what a Shopify website costs.

Margins: which channel keeps more of each sale?

On a like-for-like order, Shopify usually keeps more of the sale. A Shopify order paid through Shopify Payments loses a card fee of a few percent. The same order on Amazon loses a referral fee (often 15%), plus FBA fulfillment and storage if Amazon ships it.

But per-order fees are only half the picture. On Shopify, you pay to acquire the visitor. If you spend heavily on Meta or Google ads to drive a first purchase, your acquisition cost per order can easily exceed Amazon's referral fee. On Amazon, much of the demand is already there, though most brands also run Amazon Ads to stay visible, which adds its own cost per order. Structuring those campaigns around margin rather than revenue is central to how we run Amazon marketing.

The honest way to compare is contribution margin per order on each channel: price, minus product cost, minus platform and payment fees, minus fulfillment, minus advertising per order. Our break-even ROAS guide walks through the same maths for paid media.

Customer data and brand control

This is where the two models differ most.

• On Shopify, you own the customer. You get names, emails, addresses (with consent for marketing where required), full order history and analytics. You can build email and SMS flows, loyalty programs, subscriptions and bundles, and your repeat customers come back to you, not to a marketplace.
• On Amazon, Amazon owns the customer. You see orders and aggregated reports, but you cannot market to Amazon buyers outside Amazon. Repeat purchases happen on Amazon, under Amazon's rules, often next to competitors' sponsored listings.
• Brand presentation. A Shopify store is fully yours: design, copy, checkout branding, content. On Amazon, every product page follows the same template. Brand Registry unlocks A+ Content, a Brand Store, Sponsored Brands ads and Brand Analytics, which help, but you are still a seller inside someone else's store.

Brand Registry requires a pending or registered trademark for your brand name or logo, and the brand must appear on your products or packaging, according to Amazon's Brand Registry page. If you plan to sell on Amazon seriously, file the trademark early.

Traffic: built-in demand vs demand you create

Amazon's main advantage is the shoppers. Amazon says more than 60% of sales in its store come from independent sellers, which shows how much third-party volume the marketplace carries. When someone searches Amazon for a product type, they are often ready to buy, and if your listing ranks or your ad shows, you get a shot at that sale without building an audience first. Winning that visibility usually takes a mix of listing work and Amazon Ads, which is what our Amazon marketing service covers.

Shopify has no built-in marketplace demand. You drive every visitor through organic search, paid search and shopping ads, social, email, creators and word of mouth. That takes longer and costs more upfront, but the traffic and the customers you acquire become an asset you own. Strong DTC brands use Amazon to capture people who already know what they want and Shopify to build the brand those people searched for.

When to choose Amazon, Shopify, or both

If you are still choosing a store platform rather than a channel, our WooCommerce vs Shopify comparison covers that decision.

How to run Amazon and Shopify together

Running both channels well comes down to three connections: listings and inventory, fulfillment, and checkout.

1. Sync listings and inventory with Marketplace Connect

Shopify's Marketplace Connect app links your Shopify catalog to marketplaces including Amazon, so you can manage listings, inventory and orders from the Shopify admin. Shopify's pricing page lists marketplace orders as free up to 50 synced orders per month, then a 1% fee capped at $99 per month. Amazon still charges its own referral and fulfillment fees on those orders.

2. Use Amazon Multi-Channel Fulfillment for Shopify orders

If your inventory already sits in Amazon's warehouses for FBA, Multi-Channel Fulfillment (MCF) lets Amazon ship your Shopify orders from the same stock. Amazon's MCF app for Shopify is free to install, sends orders from Shopify to Amazon automatically, returns tracking to the Shopify admin, and ships orders in unbranded packaging at no extra cost. You pay MCF fulfillment fees per order, so compare them against your current 3PL.

3. Add Buy with Prime to your Shopify checkout

Buy with Prime lets US shoppers use their Prime membership on your Shopify store, with Prime delivery fulfilled by Amazon. Amazon describes Buy with Prime pricing as pay-as-you-go, with a Prime service fee and payment processing based on order value, plus a per-unit fulfillment fee; FBA fees apply to storage. Amazon also notes its payment processing fees do not apply when you use the Buy with Prime app for Shopify, though Shopify's own payment fees still do. It is a US-only feature and can run alongside MCF. Check the current rate card on Amazon's Buy with Prime pricing page before you turn it on.

Keep pricing and brand consistent

• Keep prices aligned. Big gaps between your Shopify and Amazon prices confuse customers and can affect your Amazon offer's visibility.
• Use Shopify for the full story. Bundles, subscriptions, loyalty and exclusive products give customers a reason to buy direct.
• Measure each channel on contribution margin, not revenue. A sale on Amazon and a sale on Shopify are not worth the same.

Amazon listing optimization: how to convert more Amazon traffic

Getting traffic on Amazon is only half the job. Your listing is your product page, and it competes with the listings and ads around it. Amazon listing optimization is the work of improving that page so more shoppers who see it click, and more who click buy. This is the focus of our Amazon CRO service. Here is where to start.

Titles

Lead with what the shopper is searching for: brand, product type, then the key differentiator (size, quantity, material, model). Amazon enforces title rules on length, repeated words and special characters, and it has tightened them recently, so check the current style guide for your category in Seller Central before rewriting. Write for the mobile search result, where only the start of the title is visible.

Images and video

The main image is what wins the click in search results. Amazon requires a pure white background for main images. Use the remaining image slots to do the selling: product in use, scale, key features called out, what is in the box, and a comparison or benefits graphic. Add a product video if your category allows it. Most Amazon shopping happens on phones, so check every image at phone size.

Bullets, description and backend keywords

Bullets should answer the questions a shopper would otherwise ask: what it does, what it is made of, how it fits, how it compares, and what is guaranteed. Lead each bullet with the benefit. Put relevant search terms you could not fit naturally into the backend search term field rather than stuffing them into the title.

A+ Content and Brand Store

With Brand Registry, you can replace the plain description with A+ Content: enhanced images, comparison charts, brand story modules and video. Amazon's Brand Registry page states that well-implemented Premium A+ Content can increase sales by up to 20%, based on Amazon internal data. Use comparison modules to move shoppers between your own products rather than to a competitor's. A Brand Store gives you a free multi-page storefront on Amazon for your range.

Reviews and ratings

Ratings and review count are among the strongest conversion signals on Amazon. Earn them legitimately: use Amazon's Request a Review button, enrol eligible new products in Amazon Vine (available with Brand Registry), and fix the product or listing issues that recurring negative reviews point to. Never offer incentives for reviews outside Amazon's approved programs; Amazon prohibits it and can remove listings or suspend accounts.

Pricing, coupons and the Buy Box

When several sellers offer the same product, only one wins the Featured Offer, usually called the Buy Box, which holds the main Add to Cart button. Amazon weighs total price including delivery, delivery speed, stock availability and seller performance. For a brand that is the only seller of its products, the work is protecting that position: stay in stock, keep fulfillment metrics healthy, keep your Amazon price in line with other channels, and stop unauthorised resellers. Coupons and deals can lift conversion when they show as a badge in search, but build them into your margin model first.

Test and measure

Brand-registered sellers can use Amazon's Manage Your Experiments tool to A/B test titles, main images, bullets and A+ Content on eligible listings. Pair it with Brand Analytics search data to see which terms drive impressions and purchases. Change one thing at a time and let tests run long enough to reach a result. If your Amazon traffic is healthy but sales lag, an Amazon listing audit is usually a cheaper win than more ad spend.

For your own store, our Shopify CRO service applies the same thinking to product pages and checkout, and our 2026 conversion rate benchmarks give you a reference point.

Common mistakes when adding Amazon to a Shopify brand

• Listing without a trademark. No trademark means no Brand Registry, no A+ Content, and less protection against hijackers.
• Ignoring fees per SKU. Some products are profitable on Shopify and loss-making on Amazon. Check before listing the whole range.
• Treating Amazon as set and forget. Listings, ads, inventory and reviews need ongoing management or the listing slips.
• Running out of FBA stock. Stockouts cost sales immediately and can hurt your ranking and offer visibility after you restock.
• Letting Amazon replace your own store. Keep investing in Shopify, email and brand so you are not dependent on one marketplace's rules and fees.