Can you sell on Amazon and keep your Shopify store?
You do not have to choose between the two. Your Shopify store stays your home base — your brand, your checkout, your customer list — and Amazon becomes a second storefront that pulls from the same catalog.
Most guides stop at "add the sales channel and sync inventory." That is the easy part. The harder question is whether the extra sales are worth Amazon's cut, and what a second channel does to the store you may one day sell. This article covers both.
If you are weighing this partly because you want a more valuable, more sellable business, it helps to start from what buyers actually pay for. Our Shopify store valuation guide walks through the profit-times-multiple math that a second channel can move.
How the connection actually works now
Here is the detail nearly every ranking article gets wrong: Shopify retired its own native Amazon sales channel back in 2023. The replacement is a first-party app called Shopify Marketplace Connect — the app formerly known as Codisto, per Codisto's own migration notice. If a blog tells you to "add the Amazon channel" from your admin as if it were built in, it is out of date.
Marketplace Connect is the bridge that keeps your Shopify catalog, prices, orders, and inventory in sync with Amazon Seller Central. It also connects eBay, Walmart, and Target Plus from the same app, so the setup you do here carries over if you expand later.
What you need before you start
- An active Shopify store with products that comply with Amazon's category rules (some categories need approval before you can list).
- An Amazon Seller Central account. You pick a plan when you register — more on the cost below.
- Product identifiers (usually a UPC/GTIN) for new Amazon listings, or the ability to match to listings that already exist.
- Store prices in a currency Amazon supports for your target marketplace.
The setup steps
- Open your Amazon Seller Central account and choose a selling plan.
- Install Shopify Marketplace Connect from the Shopify App Store and link it to your Amazon account.
- Map your Shopify products to Amazon categories, either by matching existing ASINs or creating new listings.
- Set your Amazon prices deliberately — you can offer a different price than your Shopify store.
- Turn on inventory sync so a sale on either platform decrements stock in both, which is what stops you overselling.
- Decide fulfillment: ship the orders yourself (FBM) or hand them to Fulfillment by Amazon (FBA).
What it costs: Amazon's fees and the sync app
There are two cost layers, and they stack.
The Amazon layer is the one that matters most. According to Amazon's own pricing page, the Professional selling plan runs $39.99 per month, the Individual plan charges $0.99 per item sold instead of a monthly fee, and referral fees range from 5% to 45% by category — with most standard categories landing between 8% and 15%. Fulfillment by Amazon adds separate pick-and-pack fees on top if you use it.
The sync layer is cheap by comparison. Per its Shopify App Store listing, Marketplace Connect is free to install, with the first 50 marketplace-synced orders per month free, then a 1% fee per additional synced order, capped at $99 per month. For most small stores that cap is the ceiling, not the norm.
A worked per-order example
Say you run a print-on-demand shirt store. Your Printful base cost plus shipping on one shirt is $16, and you sell it for $30. Here is what one Amazon order actually keeps, using a 15% referral fee (arithmetic, your category may differ):
- Order revenue: $30.00
- Product + shipping: −$16.00
- Amazon referral fee (15%): $30 × 0.15 = −$4.50
- Per-order gross before ads and the monthly plan: $30 − $16 − $4.50 = $9.50
Now add Amazon PPC at, say, $3.00 per order to win the sale: $9.50 − $3.00 = $6.50 left.
Compare the same shirt sold through your own Shopify store: $30 − $16 − roughly $1.20 in payment processing = $12.80, minus whatever you spend on ads. The Amazon order earns less per unit — but it reaches a buyer who may never have found your site. That trade, unit margin for reach, is the whole decision in one line.
The number that makes or breaks it is the one nobody hands you: what each order truly earns before Amazon takes its slice. If your real Shopify margin is already thin, a 15% referral fee can flip a product from profitable to break-even.
Know your true margin before you add a fee on top
Before you bolt Amazon's referral fee onto your economics, you need to know what an order actually nets today — not revenue, not a rough guess, but profit after product cost, shipping, payment fees, and ad spend. That is exactly the number PodVector is built to produce.
PodVector connects your Shopify store, your Meta Ads and Google Ads accounts, and Printify or Printful, and computes your true per-order profit from that live data. Victor, its AI employee, analyzes that data and — with your approval — takes actions on the Shopify side to act on what he finds; he does not touch your ad account, and Victor is not a dashboard. Knowing your real per-order margin first tells you whether a new Amazon channel still leaves money on the table or eats it. You can connect your store and see your true profit here.
The angle everyone skips: what a second channel does to resale value
Here is what the setup tutorials never mention. If you ever sell your store, buyers scrutinize how concentrated your traffic and revenue are — a business that lives or dies on one channel is a business one algorithm change from zero.
Adding Amazon on top of a healthy Shopify DTC business is diversification, and diversification pays at exit. According to CT Acquisitions' 2026 ecommerce valuation data, a multi-channel mix (DTC plus Amazon plus retail) adds roughly 1x to 2x to the multiple versus a single-channel store, while stores that depend on one platform trade at a discount. The same source notes an Amazon-FBA-only concentration trades 1x to 2x lower than a diversified business — so the win is Amazon alongside Shopify, not Amazon instead of it.
If exit value is part of your motivation, it is worth understanding the levers precisely. Our breakdown of the metrics buyers actually score and the methods used to value an ecommerce business show where channel mix fits into the bigger picture. When you are ready to line up buyers, where to sell your Shopify store covers the marketplaces and brokers.
When adding Amazon is not worth it
Be honest about the cases where it drags more than it lifts:
- Thin margins. If your product barely clears profit on Shopify, a referral fee in the 8%–15% range Amazon cites can wipe it out. Fix the margin first.
- Heavy brand dependence. Amazon flattens your brand into a product page. If your edge is a strong brand and repeat buyers, Amazon may commoditize you.
- Letting Amazon dominate. If Amazon grows to 80%+ of revenue, you have swapped diversification for a new concentration risk that, per CT Acquisitions, buyers discount hardest.
The sweet spot is Amazon as a meaningful-but-secondary channel that widens reach while your Shopify store stays the brand and the margin engine. If you plan to expand internationally too, our guide to selling a Shopify store across multiple countries covers the cross-border angle.
FAQs
Do I need a separate Amazon account, or does Shopify handle it?
You need your own Amazon Seller Central account — Shopify does not create one for you. Marketplace Connect only links the two accounts and syncs data between them. You choose and pay for the Amazon plan directly with Amazon.
Will selling on Amazon hurt my Shopify SEO or brand?
Not directly. Your Shopify store and its search rankings are separate from your Amazon listings. The real risk is strategic, not technical: if buyers start finding you on Amazon instead of your site, you lose the customer relationship and the email list that make a DTC brand valuable. Keep your Shopify store the destination you promote.
Can I charge a different price on Amazon than on my Shopify store?
Yes. Marketplace Connect lets you set Amazon-specific pricing, which many sellers use to build Amazon's referral fee into the number so the channel stays profitable. Just watch that you are not undercutting your own store in a way that trains customers to buy where you keep less.
Which fulfillment method should I use — FBA or ship it myself?
FBA (Fulfillment by Amazon) unlocks Prime eligibility and hands off storage and shipping, but adds per-unit fees on top of the referral fee. Fulfilling it yourself (FBM) keeps costs lower and works well for print-on-demand, where your provider already ships each order. Run the per-order math both ways before you commit.
Does adding Amazon really change what my store is worth?
It can, indirectly, by improving your traffic mix. Per CT Acquisitions, a diversified multi-channel store can command roughly 1x–2x more on its SDE multiple than a single-channel one, because buyers pay for durable, less-concentrated revenue. But it only counts if Amazon adds diversification rather than becoming your single dominant channel.