Shopify vs Amazon: Fees, Traffic, and Which Platform to Choose

Amazon and Shopify are the two dominant e-commerce platforms, but they're fundamentally different businesses. Amazon is a marketplace where buyers come to find products. Shopify is infrastructure for building your own store. Understanding what you pay on each — and what you get for it — determines which fits your business.

Amazon Fees at a Glance

Amazon Example — $40 product, small standard package, Home & Kitchen

• Referral fee: $40 × 15% = $6.00
• FBA fulfillment: $3.68
• Storage (0.06 cu ft × $0.87/12 months): $0.004 ≈ negligible
• Plan fee allocated (at 100 sales/mo): $0.40
• Total platform fees: ~$10.08 per sale (25.2%)

Add advertising (at 15% ACoS) and total platform cost rises to ~40% of sale price.

Shopify Fees at a Glance

*No transaction fee when using Shopify Payments.

Shopify Example — $40 sale, Basic plan, Shopify Payments, 100 sales/mo

• Payment processing: $40 × 2.9% + $0.30 = $1.46
• Plan fee allocated: $39 ÷ 100 = $0.39
• Fulfillment (your own 3PL or self): $5–8 depending on size
• Total platform + fulfillment: ~$7–9 per sale (17.5–22.5%)

But this excludes the cost of acquiring the customer — which on Shopify, you pay entirely yourself.

The Hidden Cost: Traffic

This is the comparison that fee tables miss:

• Amazon: 300+ million active customers search Amazon daily. You pay Amazon's high fees partly for access to that audience. Customer acquisition is built into the referral fee.
• Shopify: Zero built-in traffic. You pay for every customer via Facebook ads, Google ads, SEO, influencers, or email. Customer acquisition cost (CAC) for e-commerce brands is typically $15–50 per new customer — often exceeding the margin on a first purchase.

On a fully loaded basis (including CAC), Amazon's fees are often competitive with Shopify for new customer acquisition. The economics favor Shopify only once you have repeat customers who come back without paid acquisition.

Brand Control

Which Should You Choose?

Start with Amazon if:

• You're launching a new physical product and need sales velocity fast
• Your product fits Amazon's catalog (most physical goods do)
• You want FBA to handle fulfillment and customer service
• You don't have an existing audience to drive to a Shopify store

Choose Shopify if:

• You have an existing social following, email list, or marketing channel
• You sell custom or made-to-order products Amazon can't stock
• Brand experience and customer relationships matter (supplements, beauty, apparel)
• You want subscription, bundles, or custom checkout flows

Use both if you're scaling: Amazon for discovery and new customers, Shopify as your long-term branded channel for repeat buyers.

Frequently Asked Questions

Is it cheaper to sell on Shopify or Amazon?

Shopify has lower per-transaction fees, but Amazon provides built-in traffic. On a fully-loaded basis including customer acquisition, they're often comparable for new customers. Shopify wins for repeat buyers who don't need paid acquisition.

What fees does Amazon charge sellers?

Referral fee (8–17%), FBA fulfillment ($3.06+/unit), storage fees ($0.87–$2.40/cu ft/month), and $39.99/month for the Professional plan. Total is typically 25–40% of selling price before advertising.

Can I sell on both Amazon and Shopify?

Yes — and many growing brands do. Use Amazon for acquisition, Shopify for retention and brand building.