You made $50,000 in sales last month. Amazon deposited $32,000. Where did $18,000 go?
Amazon fees include referral commissions, storage fees, fulfillment fees, advertising costs, and long-term storage charges that stack up fast. Most sellers underestimate the total take and price products based on gross revenue instead of net profit.
Without accurate fee tracking, you lose visibility into which products actually make money or if your margins can survive a price war.
This guide shows you how to calculate Amazon fees at every stage, build profit-first pricing strategies, and automate fee reconciliation so your accounting reflects true profitability.
Amazon fees silently erode up to 40% of gross revenue for the average seller. Many sellers focus on top-line sales, only to discover that after fees, their take-home is far less than expected.
Reddit post about Amazon fees
For example, a seller with $100,000 in sales may see only $60,000 left after Amazon fees, before even accounting for product costs.
Profit-first planning means focusing on net profit after all fees, not just revenue. Most sellers underestimate the true impact of fees until it is too late. To protect your margins, you need to know exactly where your money goes.
Suggested read: From Amazon to Webgility: Tales from an Ecommerce Pro
Amazon’s fee structure is complex but predictable if you know what to look for. There are five mandatory fees and more than a dozen optional or situational charges. Understanding each is the first step to protecting your profit.
Suggested read: Large Amazon Seller’s Guide to Expanding Product Lines
Choosing the right plan can save you thousands if you know your break-even point and feature needs. Amazon offers two main plans:
Break-even example: If you sell more than 40 items per month, the Professional plan is more cost-effective.
Professional plan unlocks:
As your sales and channels expand, tracking fees manually becomes a major bottleneck.
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Tracking fees across Amazon, Walmart, Shopify, and eBay quickly becomes unsustainable as order volume grows.
Without automated reconciliation, sellers spend dozens of hours each month piecing together payout reports, fee breakdowns, and settlement data from multiple platforms.
Most never gain clear visibility into which channels or products actually drive profit.
Danwidth, an accounting consultant serving ecommerce businesses, saw his clients drowning in manual reconciliation work.
After implementing Webgility, his clients gained complete visibility into channel-specific profitability and recovered hidden costs that were eroding margins.
They could finally see how much profit or loss they were making in each channel.
His clients collectively saved nearly 1,000 hours of busywork in the first few months of 2021, and that time went straight into strategic growth activities.
Sellers using accounting automation tools like Webgility reconcile payouts, fees, and COGS in real time, eliminating hours of manual work and revealing true margins by channel and SKU.
Save up to 90% of time on reconciliation and month-end close.
Amazon referral fees vary by category, and fulfillment choices (FBA vs. FBM) add another layer of complexity.
|
Category |
Referral fee |
FBA fulfillment fee (Std. size) |
FBM shipping (Est.) |
|
Books |
15% |
$3.27-$3.98 |
$2-$4 |
|
Electronics |
8% |
$3.27-$6.15 |
$3-$6 |
|
Apparel |
17% |
$3.27-$4.25 |
$2-$5 |
|
Jewelry |
20% |
$3.27-$4.25 |
$2-$5 |
|
Toys |
15% |
$3.27-$4.25 |
$2-$5 |
Table 1: Amazon fees breakdown
Here is a scenario. A $20 toy sold via FBA:
Same toy via FBM:
Automated fee mapping tools break down profitability by SKU and fulfillment method.
Even if you optimize for category and fulfillment, hidden fees can still erode your profit.
Suggested read: Amazon Seller Accounting Software Guide
Ignoring hidden fees can wipe out your margin, making proactive tracking and inventory management your best defense. Key hidden fees include:
Checklist:
A seller with 100 units sitting 365+ days pays $690 in long-term storage fees, often more than the inventory is worth.
Strategies:
Regular, automated reconciliation flags unexpected fees before they erode your margins.
To avoid surprises, you need a system for calculating true profit after every fee.
Suggested read: How to Increase Sales on Amazon
Profit-first sellers use a repeatable framework to calculate and monitor true margins. Here is the 5-step Amazon profit audit:
For example, $10,000/month seller in electronics (FBA, 200 units):
Once you know your true profit, you can start to optimize your fee structure for even better margins.
Data-driven sellers use real-time insights to bundle, price, and manage inventory for maximum profit. Here are seven tactics:
Dashboards that break down fees and profit by channel and SKU help you prioritize where to invest.
To implement these tactics at scale, you need a system that brings all your data together.
Suggested read: QuickBooks Class Tracking for Multi-Channel Ecommerce
Webgility brings all your Amazon fees, orders, and payouts into one real-time dashboard so you can track true profit as you grow.
Key features include:
Webgility connects Amazon, Shopify, Walmart, and accounting tools like QuickBooks and Xero, so you always know your true profit. Your financial data stays up to date in real time, your reconciliation happens automatically, and you can make pricing decisions based on actual margins rather than guesswork.
Book a demo with Webgility today.
Use automation tools like Webgility to sync fees, orders, and payouts into a single dashboard for real-time profit visibility.
If you sell more than 40 items per month, the Professional plan usually saves you money and unlocks extra features.
Most Amazon sellers achieve 15-20% net profit margins after fees, but this varies by category and optimization.
Hidden fees like long-term storage, seasonal surcharges, and refund administration can quickly erode profits if not tracked and managed proactively.