Shopify vs Amazon: Your Own Store, the Marketplace or Both
Shopify and Amazon solve different problems. Amazon brings shoppers who are already searching for a product and takes a referral fee of roughly 8% to 15% on most sales; your Shopify store costs a monthly plan fee and keeps the customer, the brand and the data, but you have to bring the visitors yourself. Many brands run both: Shopify Marketplace Connect lists your Shopify products on Amazon and syncs orders and inventory back to one admin, free for the first 50 marketplace orders a month.
Amazon’s fees come from its selling plans page, Marketplace Connect facts from the Shopify Help Center and its App Store listing, all read on October 23, 2026.
Shopify and Amazon side by side
| Your Shopify store | Amazon | |
|---|---|---|
| Where buyers come from | You bring them: search, ads, social, email | Amazon’s own shoppers searching on Amazon |
| Main costs | Monthly Shopify plan, payment processing, apps; a third-party payment provider adds a transaction fee | Professional plan $39.99/month, or $0.99 per item on the Individual plan, plus a referral fee per sale |
| Fee per sale | Payment processing | Referral fee by category, mostly 8% to 15% with a $0.30 minimum; clothing tiered from 5% to 17%; media items 15% plus a $1.80 closing fee |
| Fulfillment | You or your 3PL ship | You ship, or pay Amazon to store and ship with FBA |
| Your brand | Your design, your domain, your content | Amazon’s product page layout, with limited brand space |
| Customer relationship | The customer is yours: email, account, marketing consent | Amazon handles the buyer relationship and sets the rules for contacting buyers |
| Pricing control | You set prices, discounts and bundles freely | You compete on the same product page with other sellers of the same item |
| Rules | Shopify’s terms and the law | Amazon’s seller policies on top, including listing and performance standards |
The decision usually comes down to two lines in this table. Who brings the buyer: on Amazon the demand already exists and you pay a share of each sale for it; on Shopify you pay for traffic up front with ads or content, and every repeat order after that costs you no commission. Who owns the customer: an Amazon buyer is Amazon’s customer, so you cannot simply add them to your email list, while a Shopify buyer who agreed to marketing is on your list.
A worked example with Amazon’s published numbers: a $40 kitchen product with a 15% referral fee pays Amazon $6 per sale, plus the Professional plan’s $39.99 a month. Selling the same product from your store, the $6 stays with you apart from your own payment processing fee, but you pay to bring the visitor, and if your cost per order from ads is above $6, Amazon is cheaper for that sale.
Running both from Shopify
Shopify’s own Marketplace Connect app (formerly Codisto) connects your Shopify catalog to marketplaces and keeps everything in your admin:
- Marketplaces: Amazon, eBay, Target Plus (US only) and Walmart (US only). New Etsy connections can’t be made at the moment; stores already connected to Etsy through the app can keep using it.
- Sync: listings, orders and inventory are managed in Shopify, and changes to products and orders in your store sync to the marketplaces automatically. One stock count covers both channels, so a unit sold on Amazon is no longer available in your store.
- Currency: built-in conversion shows prices in each marketplace’s local currency.
- Cost: free to install; the first 50 marketplace-synced orders a month are free, then 1% per synced order, capped at $99 a month. Amazon’s own fees still apply. The app had a 4.1 rating from 2,129 reviews on October 23, 2026.
Before you connect, check two things. Your product data must meet Amazon’s listing requirements (identifiers, categories, images), and your margins must survive Amazon’s referral fee plus Marketplace Connect’s 1% once you pass 50 orders a month. Our guide to Shopify multichannel selling covers the other channels you can add the same way.
Which to start with
How we would decide:
Start on Amazon (and keep a basic Shopify store) if your product is something people already search for by name on Amazon, you can win on price or reviews against similar products, and you do not yet have a way to bring traffic.
Start on Shopify if your product needs explaining, has a story or design people buy into, or sells better with content, creators or email. Also if margins are thin: a 15% referral fee on a product with a 25% margin leaves little room for ads.
Run both if you already sell on one and the other adds buyers without hurting it. A common split is Amazon for first purchases and your own store for repeat orders, subscriptions and bundles.
Whichever you choose, keep the Shopify store as the place where customers can join your email list. Bringing visitors to your own store is the work of content marketing and social media advertising; the marketing and SEO hub lists the rest.
Frequently asked questions
Is it cheaper to sell on Shopify or Amazon? That depends on what you pay to bring a buyer. Amazon charges a Professional plan of $39.99 a month plus a referral fee, mostly 8% to 15% per sale. Shopify charges a monthly plan and payment processing, but you pay separately for the traffic that Amazon would bring.
Can I sell on Amazon through Shopify? Shopify’s Marketplace Connect app lists your Shopify products on Amazon and syncs listings, orders and inventory. The first 50 synced orders each month are free, then 1% per order, capped at $99 a month.
Do I own my customers on Amazon? Amazon controls the buyer relationship and how you can contact buyers. On your Shopify store, customers who agree to marketing can receive your emails and offers.
Does Marketplace Connect work with Etsy? New connections to Etsy aren’t possible in October 2026. Stores that already sell on Etsy through Marketplace Connect can continue.