Amazon vs Shopify: Which Platform Costs More in 2026?
Agentis analysis of Amazon's and Shopify's own published fee schedules shows Amazon FBA sellers typically surrender 35-55% of revenue to referral fees, fulfillment, and mandatory advertising, versus 22-40% total cost-to-sell on Shopify Plus. Most merchants underestimate that gap because they compare platform fees alone.
By Herzel MishelFounder, AgentisLast reviewed
Side-by-side comparison of total selling fees on Amazon FBA vs Shopify Plus including platform fees, fulfillment, advertising, and payment processing.
See exactly where your store lands against these benchmarks.
Why This Matters
Channel economics determine where each dollar of revenue goes. Amazon takes 35-55% of revenue in total fees (referral + FBA + advertising), while Shopify Plus total cost-to-sell ranges from 22-40%. Understanding total fee burden by channel prevents the illusion of profitability on high-revenue, low-margin channels.
Benchmark Data
Download CSVData reviewed August 7, 2026.
| Tier / Category | Range | Notes |
|---|---|---|
| Amazon FBA (Referral + Fulfillment) | 30-45% | Referral fee (8-15%) + FBA fulfillment ($3-$8/unit) + storage fees |
| Amazon Advertising (PPC) | 8-15% | Required to maintain visibility; ACoS rising 10-15% annually |
| Shopify Plus (Platform + Payments) | 2.5-3.5% | Platform fee (0.25% GMV) + Shopify Payments (2.15% + $0.30) |
| Shopify Plus (Fulfillment/3PL) | 10-18% | 3PL costs vary by product size, weight, and volume tier |
| Shopify Plus (Paid Acquisition) | 10-20% | Meta, Google, TikTok spend required to drive own traffic |
How to Improve
- Calculate total cost-to-sell per channel, not just platform fees; include advertising, fulfillment, and returns
- Use Amazon for discovery and brand awareness; shift repeat customers to Shopify for higher margin
- Negotiate FBA fee tiers by consolidating shipments and optimizing product dimensions
- On Shopify Plus, check every order against your profit threshold after it is placed and before it ships
Common Mistakes
- Comparing only platform fees (Shopify 2.5% vs Amazon 15%) without including fulfillment and acquisition costs
- Assuming Amazon FBA is cheaper than 3PL without accounting for storage fees and long-term storage surcharges
- Not factoring in Amazon's mandatory advertising spend to maintain organic ranking
- Ignoring the lifetime value difference: Shopify customers are 2-3x more likely to become repeat purchasers
Methodology
Fee structures sourced from Amazon Seller Central and Shopify Plus published rates as of Q1 2026. Fulfillment and advertising ranges reflect mid-market merchant averages.
Sources
Related Calculators
Calculator
Amazon FBA Fees Calculator
Amazon FBA economics look simple on the surface and get brutal fast.
Calculator
Shopify Plus Fees Calculator
Shopify Plus merchants pay three distinct fees that most operators never combine into a single number: the platform fee (starting at 2,000 per month and scaling with revenue on large accounts), transaction fees of up to 0.15 percent for merchants not using Shopify Payments, and payment processing fees that start at 2.9 percent plus 30 cents per transaction on Shopify Payments.
Frequently Asked Questions
Is Amazon or Shopify more profitable for ecommerce merchants?
On a per-order basis, Shopify Plus is typically more profitable because total fees are lower (22-40% vs 35-55% on Amazon). However, Amazon provides built-in traffic, so the comparison depends on whether your Shopify acquisition costs are lower than Amazon's combined referral, FBA, and advertising fees. On Amazon, referral and FBA fulfillment consume 30-45% of revenue and advertising adds 8-15%, with ACoS rising 10-15% annually because paid placement is required to stay visible. On Shopify Plus, platform and payment fees are only 2.5-3.5%, but a 3PL adds 10-18% and paid acquisition adds 10-20%, since you must drive your own traffic. Shopify customers are also 2-3x more likely to become repeat purchasers, and repeat orders carry no acquisition cost. To compare for your own business, calculate total cost-to-sell per channel including fulfillment, advertising, and returns, then check whether your Shopify acquisition percentage lands below Amazon's combined take.
What are the total costs of selling on Amazon FBA in 2026?
Total Amazon FBA costs typically consume 35-55% of revenue: referral fees (8-15%), FBA fulfillment ($3-$8/unit), storage fees ($0.75-$2.40/cu ft/month), and advertising (8-15% of revenue). For a $30 product, Amazon takes roughly $12-$16 before you account for COGS. Advertising is effectively mandatory, because paid placement is required to maintain organic ranking, and ACoS has been rising 10-15% annually. Storage is the other trap: assuming FBA is cheaper than a 3PL without counting storage fees and long-term storage surcharges is a common mistake. These figures reflect Amazon Seller Central published rates as of Q1 2026, with fulfillment and advertising ranges drawn from mid-market merchant averages. Add your own referral, fulfillment, storage, and advertising costs as percentages of Amazon revenue and compare the total to the 35-55% range; if you land near the top, consolidating shipments and optimizing product dimensions to reach lower FBA fee tiers is the first lever.
Should I sell on both Amazon and Shopify?
Most mid-market merchants benefit from a multi-channel strategy, but you need per-channel profitability tracking. Use Amazon for customer acquisition and brand exposure, Shopify for retention and higher margins. The critical mistake is treating blended profitability across channels instead of managing each independently. Amazon supplies built-in traffic but takes 35-55% of revenue in referral, FBA, and advertising fees, so it works best as a discovery channel. Shopify Plus holds total cost-to-sell at 22-40%, and its customers are 2-3x more likely to become repeat purchasers, so moving repeat buyers there compounds margin over time. Blended reporting hides the risk: a high-revenue Amazon channel can look profitable in aggregate while individual orders barely clear costs once advertising is counted. Run a separate total cost-to-sell calculation per channel, compare each to its benchmark range above, and let those numbers rather than combined revenue decide where you push volume.
Related Concepts
Margin Analysis
Margin Leakage
The gradual, often undetected loss of profit across many orders, driven by small per-order cost overruns that compound into significant revenue erosion over time. Also called revenue leakage, a term more common in marketplace-seller (Amazon/Walmart) contexts for the same underlying pattern.
Margin Analysis
Gross Margin
The percentage of revenue remaining after subtracting the cost of goods sold, a foundational profitability metric that excludes operating expenses, taxes, and interest.
Cost Management
Landed Cost
The total cost of a product delivered to the customer, including COGS, freight, duties, tariffs, insurance, and handling fees.
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Go beyond Shopify's native reporting. Agentis computes true net margin on every Shopify Plus order within 60 seconds, using live NetSuite COGS, freight, fees, and FX, and flags or holds below-margin orders before they ship.
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