Most e-commerce sellers know their product costs. Far fewer know their true take-home margin after every platform, payment processor, and carrier has taken their cut.
The gap between gross margin and net margin in e-commerce is consistently larger than new sellers expect — and consistently larger than experienced sellers track. The fees are real, they compound, and they vary significantly by platform and price point.
The Fee Stack: What's Actually Coming Out
Before building any comparison, it helps to understand the full stack of costs that apply between "customer pays" and "money lands in your bank":
- Platform fee / referral fee — the percentage the platform takes on each transaction
- Payment processing — typically 2.9% + $0.30 (Stripe, PayPal, Shopify Payments)
- Fulfillment — either FBA fees (Amazon), your own shipping cost, or third-party 3PL
- Returns — industry average return rate 20–30% in apparel, 8–15% in general goods
- Advertising spend — often 15–30% of revenue for competitive categories
- COGS — product cost, packaging, manufacturing
Ads are optional in the table below (different for everyone), but everything else is platform-determined.
Platform × Price → Net Margin Comparison
Assumptions: $15 COGS on a $40 product ($50 gross margin starting point before fees). Standard tier, US domestic. Does not include ad spend.
| Platform | Selling Price | Platform/Referral Fee | Payment Processing | Shipping/Fulfillment | Net After Fees | Net Margin |
|---|---|---|---|---|---|---|
| Amazon FBA (apparel) | $40 | $5.82 (14.5%) | Included in FBA | $4.10–7.50 FBA | $11.68–$14.58 | 29–36% |
| Amazon FBA (electronics) | $40 | $3.20 (8%) | Included in FBA | $4.10–7.50 FBA | $13.30–$17.20 | 33–43% |
| Etsy | $40 | $0.20 listing + $2.00 (5%) + $1.46 (3.65% offsite ads*) | $1.46 (3.5% + $0.25) | Seller-arranged (~$6) | ~$11–14 | 28–35% |
| Shopify (Basic) | $40 | $0 platform | $1.46 (2.9% + $0.30) | Seller-arranged (~$6) | ~$17–18 | 43–45% |
| eBay (standard) | $40 | $5.32 (13.3% final value) | Included in eBay payments | Seller-arranged (~$6) | ~$13–14 | 33–35% |
*Etsy offsite ads mandatory for sellers over $10K/year revenue.
The Shopify vs. Amazon Tradeoff
Shopify's lower fees are real — but the comparison omits two critical costs:
Customer acquisition: Amazon provides built-in traffic. Shopify does not. Most DTC brands spend 20–40% of revenue on paid acquisition (Meta, Google, TikTok ads). Including even 20% acquisition cost: Shopify net margin collapses to 23–25% — comparable to Amazon FBA.
Fulfillment infrastructure: Amazon FBA handles pick, pack, ship, and returns. Shopify sellers either handle this themselves (time) or use a 3PL (typically $3–8 per order depending on weight and volume).
The real comparison isn't Shopify fees vs. Amazon fees. It's total cost to acquire + fulfill a customer, on each platform.
The Return Rate Problem
Returns are the hidden margin killer that fee calculators ignore.
Industry average return rates:
- Apparel: 20–30%
- Consumer electronics: 12–15%
- Home goods: 8–12%
- Books/media: 3–5%
Amazon FBA return processing incurs a restocking fee ($2.20–$11.05 per unit, depending on size) plus the original FBA fee is not refunded. A returned item costs the seller $6–18 per occurrence in fees alone, before considering whether the item is resellable.
At a 25% return rate in apparel, effective net margin drops 8–12 percentage points from the pre-return calculation.
What Changes at Different Price Points
Fee structures affect margin differently at different price points. The fixed component of fees (Etsy listing fee, Stripe's $0.30 flat charge, minimum FBA fees) punishes low-price items. Percentage fees punish high-price items.
The sweet spot for most platforms is $25–$75 products — high enough that fixed fees are a small percentage, low enough that percentage fees don't consume a large absolute dollar amount.
Below $15 selling price: fees often consume 40–60% of revenue, making genuine margin nearly impossible on competitive platforms.
Above $200: percentage fees become very large in absolute terms, and return risk (higher for high-ticket items) becomes a significant financial exposure.
Calculate It Yourself
The Profit Margin Calculator runs your full fee stack across any platform and price point — enter your product cost, selling price, and platform, and see exactly what you'll net per unit before and after returns.