Is Amazon FBA better than Shopify?

Neither is better for every brand. Amazon FBA is better for fast sales in categories with existing search demand. Shopify is better for brand control, customer data and higher margin per order. Many brands launch on one and add the other within a year.

Is Shopify cheaper than Amazon FBA?

Shopify's platform fees are usually lower than Amazon's referral and FBA fees, but you pay for traffic yourself through ads, content and email. Once marketing is included, the cost per order can be similar or higher, especially for a new brand without an audience.

Can I use Amazon FBA to ship Shopify orders?

Yes. Amazon's Multi-Channel Fulfillment can ship orders from your Shopify store using your FBA inventory, and Buy with Prime lets you offer Prime delivery on your own site. Both carry Amazon fees, including a 3.5% fuel surcharge from May 2, 2026.

Should a new brand start on Amazon or Shopify?

Start on Amazon if shoppers already search there for your product and your margins can carry the fees. Start on Shopify if your product needs storytelling, subscriptions or a community. Either way, plan inventory and pricing so a second channel can be added later.

Do I own my customers on Amazon?

Not in the way you do on Shopify. Amazon owns the customer relationship and limits how you can contact buyers. Brand registered sellers get tools such as Brand Stores and some tailored promotions, but email lists and full customer data stay with your own store.

Amazon FBA vs Shopify in 2026: Costs, Traffic and Control

What changed: Marketplace selling with FBA compared with your own Shopify store
When: Updated October 2026
Who it affects: New brands and DTC brands deciding where to sell
What to do: Start where your demand is, then add the second channel

Key takeaways

Amazon FBA sells to shoppers who already search; Shopify needs you to bring every visitor.
Amazon charges per sale plus FBA fees; Shopify charges a plan, payment fees and your ad spend.
Most brands win with both: Amazon for volume, Shopify for customers and margin.

Amazon FBA vs Shopify

	Amazon FBA	Shopify
Traffic	Built-in search demand	You bring it
Main fees	Referral plus FBA	Plan plus payments
Customer data	Limited	Full
Fulfillment	Amazon ships	You or 3PL
Brand control	Listing and Store	Everything

Amazon FBA vs Shopify at a glance

Amazon is a marketplace. You list products in a shared catalogue, compete on the same page as other sellers and pay Amazon a share of each sale. FBA adds Amazon storage and shipping. Shopify is software for running your own online store. You choose the design, set the checkout and own the customer list, but Shopify brings no shoppers by itself.

Neither is better in general. The right choice depends on whether your product already has search demand on Amazon, how much you want to spend on marketing and how much control your brand needs. If you are just starting, our guide on how to start an Amazon business covers the Amazon side.

Cost comparison

The cost structures are very different. Amazon takes a percentage of each sale; Shopify charges a subscription and payment fees, and you pay for traffic yourself.

Amazon: Professional plan at $39.99 per month
Amazon: referral fee per sale, 15% in many categories
Amazon FBA: per-unit fulfillment fee, monthly storage and a 3.5% fuel surcharge since April 17, 2026
Shopify: monthly plan (Basic, Grow, Advanced or Plus) plus card processing
Shopify: extra transaction fee if you use a third-party payment provider, listed at 2% on Basic down to 0.6% on Advanced
Shopify: apps, themes and your own shipping or 3PL costs
Shopify: paid ads, email and content to bring in every visitor

Traffic: the biggest difference

On Amazon, shoppers arrive with intent. They search for a product type, compare a few options and buy. Good listings and Amazon PPC management can put you in front of them on day one.

On Shopify, nobody visits unless you send them. Brands rely on Meta and Google ads, search engine optimisation, email, influencers and social content. Customer acquisition costs are often higher at first, but every customer you win is yours to market to again.

Brand control and customer data

Shopify wins on control. You design the full experience, set your own prices and promotions, collect email addresses and build a customer list you can reach any time.

Amazon limits all of that. You control the listing content and Brand Store if you are brand registered, but Amazon owns the customer relationship, restricts contact with buyers and expects competitive pricing. Other sellers can also list on your product page, which makes Amazon brand protection important.

	Amazon FBA	Shopify
Shoppers already searching
Own the email list
Prime delivery built in
Set any price or offer

Most brands use both channels.

Fulfillment: FBA vs doing it yourself

FBA takes storage, packing, shipping, returns and customer service off your hands and gives your Amazon offers Prime eligibility. Since January 1, 2026, US sellers must prep and label inventory themselves before it goes to Amazon.

Shopify stores ship orders themselves or through a 3PL. You can also use Amazon's Multi-Channel Fulfillment to ship Shopify orders from FBA stock, or add Buy with Prime to your site. Both carry the 3.5% fuel and logistics surcharge from May 2, 2026.

Pros and cons of each

A quick summary of where each channel is strong and weak.

Amazon FBA pros: built-in demand, Prime trust, fast launch, Amazon-run fulfillment
Amazon FBA cons: fees on every sale, little customer data, price pressure, policy risk
Shopify pros: full brand control, customer data, higher margin per order, flexible offers
Shopify cons: you buy all traffic, slower start, you run checkout, service and fulfillment

Which should you start with?

Start with Amazon if people already search Amazon for your product type, if you want sales quickly and if your margins can carry referral and FBA fees. Start with Shopify if your product is new, needs a story to sell, depends on subscriptions or bundles, or targets a niche you can reach through social media.

Either way, plan for the second channel early. A brand that sells on both can use Amazon for volume and discovery and Shopify for repeat customers and higher margin. See our guide to Shopify pros and cons for more on the DTC side.

How to run Amazon and Shopify together

Running both works best with a few rules.

Keep prices consistent so you do not undercut yourself
Use one inventory forecast across both channels
Consider Multi-Channel Fulfillment so one FBA stock pool serves both
Send some paid social traffic to Amazon with Attribution tags to measure it
Use Shopify for bundles, subscriptions and exclusive products

1Pick channel one
Where demand already is
2Align prices
No self-undercutting
3Share stock
One forecast, MCF option
4Add channel two
Bundles and subscriptions

Where PPC Spider helps

PPC Spider manages both sides. Our Shopify DTC agency team builds and grows Shopify stores, and our Amazon team runs listings and ads with SpiderOS monitoring bids, budgets, search terms and stock. Compare fulfillment choices in our FBA vs FBM guide, or see plans on our agency pricing page.

Sources

Amazon: Selling on Amazon fees and pricing (sell.amazon.com/pricing)
Shopify: Pricing plans (shopify.com/pricing)
PPC Land: Amazon's 3.5% fuel surcharge is coming, April 2026 (ppc.land/amazons-3-5-fuel-surcharge-is-coming-and-sellers-are-furious/)

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