The Fee Structures: Side by Side
| Fee Type | Amazon FBA | Shopify |
|---|---|---|
| Platform / Referral Fee | 15% of sale price | $0 |
| Payment Processing | Included in referral | 2.9% + $0.30 |
| Fulfillment | $3.22–$8.35 (FBA) | Your 3PL / $1.50–$5 |
| Monthly Platform Fee | $39.99 (Pro) | $39–$399 |
| Storage Fees | $0.87/cubic ft (Q1–Q3) $2.40/cubic ft (Q4) | None |
| Traffic / Ad Cost | Organic available | Fully paid (Meta, Google) |
| Brand Control | Limited | Full |
| Repeat Purchase Economics | Amazon owns the customer | You own the customer |
Real Example: $50 Product, $12 COGS
Profit Per Unit Breakdown
Cost ItemAmazon FBAShopify
Selling Price$50.00$50.00
Unit Cost (COGS)−$12.00−$12.00
Shipping to Platform−$2.00−$5.50
Platform / Referral Fee−$7.50−$0
Fulfillment Fee−$5.40−$1.50
Payment Processing−$0−$1.75
Return Rate (10%)−$5.00−$5.00
Ad Spend / Customer Acq.−$4.00−$12.00
True Profit Per Unit$14.10$12.25
In this scenario Amazon FBA wins by $1.85/unit — but only because of lower CAC. A Shopify store with a repeat customer LTV of even 2x changes this calculation completely.
When Amazon FBA Wins
Amazon FBA
Best For Commodity Products
High search volume, price-sensitive buyers, no brand loyalty. Amazon's built-in traffic offsets the 15% fee when your paid CAC would be $15+ per order anyway.
Shopify
Best For Brand-Led Products
Strong creative differentiation, subscription or repeat purchase potential, email list building, and premium positioning. You own the relationship — and that compounds.
The LTV Factor: Why Shopify Can Outperform Long-Term
Amazon's single biggest hidden cost is customer ownership. When a customer buys from you on Amazon, they are Amazon's customer. Every repeat purchase costs you another 15%+ referral fee. On Shopify, a customer you acquire once can buy 5 more times at near-zero CAC — flipping the long-term economics entirely.
Our tool models this with the LTV Strategy tab: input your repeat purchase rate and see how your 6-month customer value changes the allowable CAC on your first order.
Run the Numbers for Your Product
Toggle between Amazon FBA and Shopify in seconds. See exactly where your margin goes on each platform.
Open Platform Comparison Tool →Frequently Asked Questions
Is Amazon FBA or Shopify more profitable?
It depends on your product and CAC. Shopify has no referral fee but you pay for every customer via ads. Amazon FBA charges 15% + FBA fees but organic traffic can offset this. For branded products with repeat buyers, Shopify typically wins on LTV. For commodity products, Amazon can win on first-order economics.
What are Amazon FBA's total fees on a $50 product?
On a $50 product: 15% referral fee = $7.50 + average FBA fulfillment of ~$5.40 = $12.90 in platform fees alone (25.8% of revenue). Q4 storage surcharges and aged inventory fees can add more.
Can I sell on both Amazon and Shopify?
Yes — and many 7-figure brands do. Use Amazon for customer acquisition and Shopify for repeat purchase retention. The key is to not cannibalize your Shopify pricing. Many sellers price on Amazon 10–15% higher to account for fees.