When founders ask me about expanding from Shopify to Amazon, a second question follows within minutes. If we list there, won’t our best customers just start buying on Amazon instead?
It’s a fair worry. Amazon remains the first stop for a majority of US online shoppers. A 2024 Jungle Scout survey of 1,000 of them found 56% started product searches on Amazon. Only 42% started on search engines like Google. That reach is the opportunity. It’s also the risk, because shoppers who discover you there can quietly move their reorders off your site.
After 25 years in marketing and 12 running an agency, here is my honest answer. Cannibalization doesn’t just happen to you. It comes from four choices you control: what you list, what you charge, how you ship and where you send your own customers.
Get those right, and Amazon becomes a channel for shoppers who were never going to find your site. Get them wrong, and you pay Amazon a referral fee on customers you already had.
Here is the playbook we use with established Shopify brands, in the order we use it.
Is selling on Amazon worth it for a Shopify brand?
For most established brands, yes, as long as you treat Amazon as an acquisition channel. That means closing the four leaks that cause cannibalization:
- Price gaps. When the same item costs less on one channel, shoppers notice, and your most loyal buyers notice first.
- Your own marketing. Amazon badges and buttons on your site push shoppers you paid to acquire toward a channel that charges you again.
- Easy reorders. Replenishment orders that used to come to your site start arriving through Subscribe & Save or Prime.
- Listing everything. Putting your whole catalog on Amazon hands over the subscription heroes and bundles that drive your lifetime value.
Notice that Amazon itself isn’t on that list. In most of the audits we run, the leak traces back to a choice the brand made. That means the brand can reverse it.
Staying off Amazon isn’t neutral, either. If shoppers search for your brand there, someone will answer: a reseller, an arbitrage seller or a lookalike product. So start with a simple test. Search your brand name on Amazon today. If you find listings you didn’t create, you’re already on Amazon. You just aren’t in control.
Then enroll in Amazon Brand Registry. It’s free, and Amazon says it helps protect your brand even if you don’t sell in its store. You’ll need a pending or registered trademark and a logo with your brand name on the product or packaging.
Step 1: Run the Shopify to Amazon math by SKU
Before you list a single product, compare what an order is worth on each channel. Amazon’s costs stack up quickly. The Professional selling plan costs $39.99 a month. Referral fees vary by category. Many, such as Home and Kitchen, pay 15%. Some lower-priced beauty and grocery items pay 8%. Then come fulfillment, storage and advertising.
Fulfillment has also gotten pricier this year. Amazon raised FBA fees by an average of $0.08 per unit in January. In April, it added a 3.5% fuel and logistics surcharge, which Amazon said works out to about $0.17 per unit for US FBA. Holiday peak fees then add an average of $0.32 per unit from October 15 through January 14, 2027. The surcharge applies on top.
Compare what one order is worth on each channel
Now put three numbers side by side for each SKU. First, what an Amazon order contributes. Second, what a repeat order on your site contributes. Third, what a new-customer order on your site contributes after acquisition cost. Here is an illustrative $40 consumable:
| Per order | Amazon (FBA) | Your site: repeat | Your site: new customer |
|---|---|---|---|
| Price | $40.00 | $40.00 | $40.00 |
| Product cost | -$10.00 | -$10.00 | -$10.00 |
| Amazon referral fee (15%) | -$6.00 | None | None |
| Payment processing (about 3%) | Included | -$1.20 | -$1.20 |
| Pick, pack and shipping | -$5.69 | -$7.00 | -$7.00 |
| Storage | -$0.10 | -$0.10 | -$0.10 |
| Ads or acquisition | -$4.80 | -$1.00 | -$30.00 |
| Contribution per order | $13.41 | $20.70 | -$8.30 |
Illustrative only. It assumes a 15% referral fee and a $5.50 FBA fee plus the 3.5% surcharge. Amazon ads run at 12% of sales. Repeat orders carry a $1 retention cost, and new customers cost $30 to acquire. Run your own SKUs through Amazon’s Revenue Calculator.
The table makes the cannibalization argument in one line. Amazon is a good deal for customers you don’t have yet and a bad deal for customers you already do. Here, every repeat buyer who moves to Amazon costs you $7.29 per order. Meanwhile, every new customer Amazon brings in is $21.71 better on the first order than one bought through paid social.
Your site still wins on lifetime value, which is why the next steps keep repeat orders at home. And if your site converts poorly, fix that first. Better conversion shrinks the acquisition cost in that third column.
Step 2: Decide which Shopify products belong on Amazon
Don’t connect your whole catalog on day one. Instead, give each product a job.
| Send to Amazon | Keep on your site |
|---|---|
| Hero products shoppers already search for on Amazon | Bundles, kits and gift sets |
| Small, light items where FBA fees stay a modest share of the price | Subscription-first products and your best subscription offer |
| Entry-level or trial sizes that introduce new customers | New launches and limited editions, so your list gets first access |
| Products resellers already sell, so you can take the listing back | Personalized, oversized or low-margin items where fees eat the order |
Channel-specific pack sizes help, too. A 2-pack on Amazon and a 3-pack on your site aren’t the same product. Shoppers can’t compare them line for line. They also give you room to price each channel on its own merits.
Be careful with Subscribe & Save if subscriptions drive your DTC economics. According to Amazon’s seller guide, you fund a 0%, 5% or 10% subscriber discount. Amazon adds another 5% when a subscriber gets five or more items in one delivery. Amazon also enrolls eligible products automatically at your default discount, so review those settings in Seller Central.
Step 3: Hold one price across Shopify and Amazon
Price gaps do the most damage, and Amazon’s rules raise the stakes. Under its Marketplace Fair Pricing Policy, Amazon monitors prices and compares them with other prices. If it sees pricing that could damage customer trust, it may remove your Featured Offer. Most sellers know that as the Buy Box.
Amazon also tracks a competitive external price. That’s the lowest price for an item at other major retailers outside Amazon. To count as competitively priced, your price plus shipping should be at or below it. Amazon doesn’t say exactly which sites it checks. So assume any public price can count, including the one on your own site.
It’s tempting to mark up Amazon prices to cover the fees. Don’t do it on identical SKUs, because a higher Amazon price can cost you the Featured Offer. Use different pack sizes to cover fees instead. Then set these rules before launch:
- One everyday price per identical SKU. Same product, same price, on both channels.
- Private promotions on your site. Use email and SMS codes from Klaviyo, loyalty rewards, gifts with purchase and free-shipping thresholds instead of public sitewide markdowns.
- Amazon promotions for Amazon shoppers. Brand Tailored Promotions let you target recent, repeat or high-spend customers on Amazon.
- Parity price rules. Marketplace Connect can set Amazon prices relative to your Shopify price, so set the rule to match.
Step 4: Connect Shopify to Amazon and choose fulfillment
The connection itself is the easy part. The settings you pick decide whether Amazon helps your site or competes with it.
How to connect Shopify to Amazon
Most brands start with Shopify Marketplace Connect, Shopify’s own app (formerly Codisto). It syncs listings, orders and inventory with Amazon, Walmart, Target Plus and eBay. Installing it is free, and so are the first 50 marketplace-synced orders each month. After that, it charges 1% per synced order, capped at $99 a month.
- Open a Professional seller account in Seller Central.
- Enroll your brand in Brand Registry.
- Install Marketplace Connect and link your Amazon account.
- Match existing ASINs or create listings with your UPCs, then map categories.
- Set default price and quantity rules, and choose FBA or merchant fulfilled.
Two details matter more than the setup. First, all sellers of a product share one Amazon listing. Only the offer, meaning price, quantity and fulfillment, is yours alone. That’s another reason to control your listings through Brand Registry. Second, set a quantity buffer so a spike on Amazon can’t sell your last units out from under your website.
Start with a handful of SKUs and check prices and inventory daily for two weeks. Recent app reviews include complaints about sync errors, and a pricing mistake on Amazon gets expensive fast.
FBA, merchant fulfilled or MCF
- Fulfillment by Amazon (FBA) earns the Prime badge, and Amazon handles shipping, returns and customer service on Amazon orders. You pay the fees above.
- Merchant fulfilled ships Amazon orders from your own warehouse or 3PL. You keep more control but give up the Prime badge by default.
- Multi-Channel Fulfillment (MCF) ships your Shopify orders from the inventory you keep with Amazon, in unbranded packaging. Amazon treats FBA and MCF stock as a single pool.
Step 5: Bring Amazon Prime to your Shopify store
Some customers will always prefer Prime. They trust the delivery promise, and Amazon already has their payment details. Buy with Prime lets those shoppers check out with Prime on your own site. As a result, the order lands in your Shopify admin instead of on Amazon.
The numbers are worth a test. Amazon reports that merchants saw a 16% average increase in revenue per shopper with Buy with Prime. That figure comes from A/B tests with 167 merchants between July 2023 and June 2024. It’s a vendor number, so measure it on your own store.
The Prime service fee is 3% of the order value, excluding tax. Since January 15, 2026, the minimum is $0.30 per order. Fulfillment and storage fees come on top. However, Amazon doesn’t charge its marketplace referral fee on these orders. Peak fees and the 3.5% surcharge apply to Buy with Prime, too.
Amazon’s MCF and Buy with Prime app manages both services, including orders and returns, from your Shopify admin. Buy with Prime requires a US-based business. Amazon also says merchants can use Buy with Prime order details, including email addresses, to provide customer service. Check Amazon’s terms and your consent settings before you add those shoppers to marketing flows.
This is also where I draw a hard line. Never put a “Buy on Amazon” button on your product pages. If Prime is why shoppers hesitate, offer Buy with Prime instead.
Step 6: Protect the customer relationship you built
On Amazon, the customer relationship belongs to Amazon. Its seller policies prohibit attempts to divert Amazon shoppers to another website or sales process, including special offers that encourage them to leave Amazon. So you won’t build your email list there, and you shouldn’t try. Some sellers still tuck a website discount into the box, but that’s a policy risk you don’t need. Keep package inserts focused on using the product well.
Instead, build loyalty on each channel with the tools that channel allows:
- On Amazon: a Brand Store, A+ Content, Subscribe & Save where it fits and Brand Tailored Promotions for repeat buyers.
- On your Shopify site: what Amazon can’t offer, like your best subscription terms, loyalty tiers, bundles and early access. Capture email and SMS consent, then send a post-purchase flow that’s more than a receipt.
- In your own marketing: no Amazon badges or links on your site, in your emails or in retargeting. Your owned audience should buy from you.
There’s one exception. Sometimes you’ll run off-Amazon ads to cold audiences who prefer Amazon, such as a creator’s followers. In that case, tag the links with Amazon Attribution. Brand-registered US sellers can then earn a Brand Referral Bonus averaging 10% of qualifying sales. Amazon credits it against future referral fees. Keep that traffic separate from your core prospecting, though, so you can see what it truly adds.
Step 7: Measure halo against cannibalization every month
Before launch, record 90 days of baseline data from your store. Track new-customer orders, returning-customer revenue, repeat purchase rate and branded search clicks in Google Search Console. Then review this scorecard every month:
| Signal | What it tells you | Healthy direction |
|---|---|---|
| Returning-customer revenue on your site | Whether loyal buyers are moving to Amazon | Flat or rising |
| New-customer orders on your site | Whether Amazon is also taking first purchases | Flat or rising |
| Amazon new-to-brand share | Whether Amazon is reaching new people | High and steady |
| Branded search clicks | Whether Amazon visibility lifts brand demand | Rising |
| Blended contribution margin | Whether total profit grew, not just revenue | Rising |
Amazon counts an order as new-to-brand when the shopper hasn’t bought your brand on Amazon in 12 months. However, Amazon can’t see your Shopify history. If your team has Amazon Marketing Cloud access, you can upload hashed customer data. Then you can see how much your existing customers overlap with the shoppers your Amazon ads reach.
A one-question post-purchase survey helps, too. Ask new buyers on your site whether they considered buying on Amazon.
The decision rule is simple. If returning-customer revenue on your site falls while Amazon grows, pull back. Fix price gaps, remove overlapping SKUs or rework your bundles. If both channels grow, add SKUs slowly.
A 90-day Shopify to Amazon launch plan
| Timing | Focus | Key actions |
|---|---|---|
| Days 1 to 30 | Protect and plan | Search Amazon for your brand and enroll in Brand Registry. Pick 5 to 10 hero SKUs, run the math and write your price policy. |
| Days 31 to 60 | Launch | Install Marketplace Connect and build listings with A+ Content. Send inventory to FBA and start Sponsored Products on branded and category terms. |
| Days 61 to 90 | Measure and decide | Review the scorecard and test Buy with Prime on hero SKUs. Then expand, hold or prune SKUs. |
One timing note. If you’re reading this in October, don’t launch in the middle of peak season. Amazon advised sellers to get holiday inventory into its network by October, and peak fees run through January 14, 2027. Use Q4 to finish Brand Registry, your SKU plan and your price policy. Then launch in mid-January, once non-peak rates return.
The bottom line
Adding Amazon to a Shopify brand isn’t really a yes-or-no decision. It’s a design decision. List the right products, hold one price and keep your best offers and customer relationships at home. Then measure the overlap every month. Do that, and Amazon adds customers you’d never reach, while your best customers keep buying from you directly.
Weighing the move from Shopify to Amazon? Our Amazon Paid Ads Management team would be glad to look at your catalog and margins with you. We’ll show you which products we’d list first and where we’d start. You can book a time with our team here.
Sources
- Practical Ecommerce. Amazon Rules Product Discovery, for Now (January 2026, citing Jungle Scout’s 2024 consumer survey)
- Sell on Amazon. Amazon Brand Registry
- Sell on Amazon. How much does it cost to sell on Amazon? Standard selling fees
- Amazon Selling Partners. Update to U.S. Referral and Fulfillment by Amazon fees for 2026
- Digital Commerce 360. Amazon to add fuel and logistics surcharges (April 3, 2026)
- Supply Chain Dive. Amazon announces 2026 holiday fulfillment fees, advises early shipping (July 13, 2026)
- Sell on Amazon. What is Amazon Subscribe & Save?
- Sell on Amazon. Amazon pricing strategies: How to price products to drive sales
- Shopify App Store. Shopify Marketplace Connect
- Shopify Help Center. Setting up and managing Amazon offers and listings
- Shopify App Store. Amazon MCF and Buy with Prime
- Amazon Supply Chain. MCF and Buy with Prime App for Shopify user guide
- Buy with Prime. Buy with Prime for business
- Buy with Prime. Pricing
- Buy with Prime Knowledge Center. MCF and Buy with Prime app for Shopify
- Buy with Prime Knowledge Center. Install the MCF and Buy with Prime app for Shopify
- Jungle Scout. Amazon Terms of Service: Prohibited Seller Activities Explained
- Sell on Amazon. Brand Referral Bonus: Drive traffic and boost your bottom line
- Amazon Ads. Sponsored Brands (new-to-brand metrics)
- AWS for Industries. Integrating CDP with Amazon Marketing Cloud to drive better Ad campaigns