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Amazon Seller Fees (2025): What They Are—and How to Book Them in Beancount

· 9 min read
Mike Thrift
Mike Thrift
Marketing Manager

Selling on Amazon is a powerful way to reach millions of customers, but the platform's fee structure can feel like a maze. If you're an operator who values clean, auditable, double-entry books, tracking these costs accurately is non-negotiable. This guide breaks down Amazon's 2025 US marketplace fees and shows you exactly how to record them using the plain-text accounting tool, Beancount.

TL;DR ⚡

2025-08-21-amazon-seller-fees-2025

  • You’ll encounter a handful of recurring Amazon charges: Selling plan, Referral, Closing (media), FBA fulfillment & storage, Inbound placement, Low‑inventory‑level, Returns processing, Refund administration, and a High‑volume listing fee for very large catalogs.
  • Keep a separate Assets:Amazon:Clearing account. Book sales and fees there; when Amazon pays out, transfer the net to your bank. This makes reconciliation a breeze.
  • Track each SKU as its own commodity (e.g., SKU:WATER-BOTTLE) so Beancount can compute your Cost of Goods Sold (COGS) by lot automatically.
  • You can reconcile quickly by importing settlement or date-range reports and mapping Amazon’s “transaction types” directly to your Beancount expense accounts.

The Amazon Fee Map (US Marketplace)

Here’s a breakdown of the most common fees you'll see in 2025.

Selling Plan Fee

This is your basic subscription fee for accessing the marketplace.

  • Individual Plan: No monthly fee. Instead, you pay $0.99 for each item you sell.
  • Professional Plan: A flat $39.99 per month, which waives the per-item charge. This is the standard choice for any serious seller. All other selling fees apply on top of this.

Referral Fee

This is Amazon's commission for each sale.

It's a percentage of the item’s total sales price (including shipping and any gift wrapping). The rate depends entirely on the product category. Most categories fall in the 8–15% band, but some use tiered rates (e.g., 15% on the first $500 and 8% on the portion above that). Certain categories also have a minimum referral fee, often $0.30. Always check the current rate card for your specific category.

Closing Fee (Media Categories)

If you sell media items like Books, Music, Video, or DVDs, Amazon charges an additional flat $1.80 per-item closing fee.

FBA Fulfillment Fees

These are the per-unit pick, pack, and ship fees for using Fulfillment by Amazon (FBA). The cost varies based on the item's size and weight. Amazon updates these rate cards periodically. For 2025, non-peak rates reverted to 2024 non-peak levels on January 15, 2025. Always consult the current FBA rate card to find your product's exact size tier and associated fee.

Monthly Storage & Aged-Inventory Surcharge (FBA)

Amazon charges for the space your inventory occupies in their fulfillment centers.

  • Monthly Storage: Billed by the cubic foot.
  • Aged-Inventory Surcharge: An additional monthly fee assessed on inventory that has been sitting in a fulfillment center for too long. This stacks on top of the regular monthly storage fee.

Inbound Placement Service Fee (FBA)

This is a per-unit fee tied to how you send inventory to Amazon. It's designed to cover the costs of Amazon distributing your products across its fulfillment network. Certain programs, like "New Selection," may temporarily exempt new products up to set limits.

Low-Inventory-Level Fee (FBA)

This fee applies to standard-size products with consistently low inventory levels relative to customer demand. Amazon measures this with a metric called "historical days of supply." If your stock level for a popular item drops below the threshold (generally 28 days), this fee kicks in.

Returns Processing Fee (FBA)

For products in categories with higher-than-typical return rates (like apparel and shoes), Amazon can charge a returns processing fee on each customer return. Some "New Selection" units are waived from this fee up to a certain cap.

Refund Administration Fee

When you issue a customer a refund for an order, Amazon gives you back the referral fee you paid. However, they keep a portion of it as a processing fee. This is the lesser of $5.00 or 20% of the referral fee for that item.

High-Volume Listing Fee (Huge Catalogs)

This fee only affects sellers with massive catalogs. If you have more than 1.5 million active SKUs, Amazon charges a monthly fee of $0.001 per eligible SKU above that threshold.

Note: Rates and policies can differ by country, region, and category. Always review your local Seller Central help pages before booking.


How These Fees Show Up in Your Reports 🧾

You can find all this data in Seller Central. The two most useful reports for accounting are:

  1. Date Range Reports (Payments → Date Range Reports): These provide a summary of your income, expenses, taxes, and net transfers for a specific period. They are perfect for high-level ledger import and reconciliation.
  2. Settlement Files (e.g., Flat File V2): These files break down every single transaction, showing the fee type, order ID, amount, and date. This is the granular data you'll use to map everything correctly.

A Beancount-First Way to Record Amazon Activity

Here’s how to translate Amazon's complex world into clean, simple Beancount entries.

1. Set Up a Minimal Chart of Accounts

First, define the accounts you'll need. This simple structure covers everything.

; --- ASSETS ---
Assets:Amazon:Clearing ; Your Amazon "wallet"
Assets:Bank:Checking ; Where payouts land
Assets:Inventory:SKU:<code> ; One sub-account per SKU

; --- INCOME & COGS ---
Income:Sales:Amazon
Expenses:COGS:Inventory

; --- EXPENSES ---
Expenses:Marketplace:Amazon:Referral
Expenses:Marketplace:Amazon:FBAFulfillment
Expenses:Marketplace:Amazon:Storage:Monthly
Expenses:Marketplace:Amazon:Storage:Aged
Expenses:Marketplace:Amazon:InboundPlacement
Expenses:Marketplace:Amazon:LowInventoryLevel
Expenses:Marketplace:Amazon:ReturnsProcessing
Expenses:Marketplace:Amazon:Other ; For misc. fees

Beancount’s ability to track inventory lots and cost basis is a superpower. You'll "buy" inventory into Assets:Inventory:SKU:... with a cost {...}. When you sell, Beancount automatically calculates the Cost of Goods Sold.

2. Book Each Sale and Its Fees

Let's record a $30 FBA sale for SKU:WATER-BOTTLE. The referral fee is $4.50, FBA fulfillment is $4.24, and you incurred a $0.15 low-inventory fee. You originally purchased this unit for $5.00.

2025-02-10 * "Amazon Order 113-2233445-6677889" "WATER-BOTTLE"
Assets:Amazon:Clearing 21.11 USD
Income:Sales:Amazon -30.00 USD
Expenses:Marketplace:Amazon:Referral 4.50 USD
Expenses:Marketplace:Amazon:FBAFulfillment 4.24 USD
Expenses:Marketplace:Amazon:LowInventoryLevel 0.15 USD
Assets:Inventory:SKU:WATER-BOTTLE -1 SKU:WATER-BOTTLE {5.00 USD}
Expenses:COGS:Inventory 5.00 USD

Why it balances: The $30 sale is credited to Income. The fees ($4.50 + $4.24 + $0.15) and the COGS ($5.00) are debited to your expense accounts. The net cash from the sale, $21.11, is debited to your Assets:Amazon:Clearing account. The inventory asset is credited (reduced by one unit), and the corresponding cost is expensed.

3. Record the Payout

When Amazon disburses your funds, the transaction is simple. You're just moving money from your Amazon "wallet" to your actual bank account.

2025-02-15 * "Amazon Payments" "Settlement disbursement"
Assets:Bank:Checking 2,500.00 USD
Assets:Amazon:Clearing -2,500.00 USD

After each payout, your Assets:Amazon:Clearing account balance should trend back toward zero. Use your date-range report totals to spot any discrepancies.

4. Handle Storage, Aged Inventory, and Inbound Placement

These fees often appear as separate lines in your settlement reports. Book them as direct debits to your clearing account.

2025-03-15 * "Amazon FBA Storage Fees" "Monthly + aged inventory"
Expenses:Marketplace:Amazon:Storage:Monthly 125.40 USD
Expenses:Marketplace:Amazon:Storage:Aged 35.20 USD
Assets:Amazon:Clearing -160.60 USD

2025-03-20 * "FBA Inbound Placement Service" "Shipment split optimization"
Expenses:Marketplace:Amazon:InboundPlacement 62.00 USD
Assets:Amazon:Clearing -62.00 USD

5. Refunds & Returns

When a customer returns a product, you reverse the sale and the COGS, and account for any non-refundable fees. For this $30 sale, let's say Amazon keeps a $0.30 refund administration fee.

2025-03-02 * "Refund 113-2233445-6677889" "Refunded WATER-BOTTLE"
Assets:Amazon:Clearing -29.70 USD ; Net debit
Income:Sales:Amazon 30.00 USD ; Reverse the sale
Expenses:Marketplace:Amazon:Other 0.30 USD ; The refund admin fee
Assets:Inventory:SKU:WATER-BOTTLE 1 SKU:WATER-BOTTLE {5.00 USD}
Expenses:COGS:Inventory -5.00 USD ; Reverse the COGS

Here, you debit Income to reverse the revenue, and credit Expenses:COGS to reverse the cost. The inventory unit is added back to your asset account. The net effect on your Assets:Amazon:Clearing is the amount refunded to the customer.


Importing & Reconciling Quickly

The key to efficiency is mapping. Export a Date Range Report or a Flat File V2 settlement report from Seller Central. Then, create a simple mapping from Amazon's transaction-type column to your expense accounts:

  • OrderIncome:Sales:Amazon
  • CommissionExpenses:Marketplace:Amazon:Referral
  • FBA-fulfillment-feeExpenses:Marketplace:Amazon:FBAFulfillment
  • StorageFeeExpenses:Marketplace:Amazon:Storage:Monthly
  • AgedInventorySurchargeExpenses:Marketplace:Amazon:Storage:Aged
  • InboundPlacementFeeExpenses:Marketplace:Amazon:InboundPlacement
  • LowInventoryLevelFeeExpenses:Marketplace:Amazon:LowInventoryLevel

For those looking to automate, Beancount’s import ecosystem (like beancount-import) is fantastic. You define the rules once, and your settlement files can be ingested into your ledger automatically.


Practical Guardrails That Save Money (and Keystrokes) 💰

  • Avoid the Low-Inventory Fee: Watch your historical days of supply. Keep enough buffer stock to meet demand, but don't overdo it and trigger aged-inventory surcharges.
  • Use New Selection Benefits: When launching new products, enroll them in the New Selection program to get temporary waivers on returns processing and inbound placement fees.
  • Check Referral Rates Before Pricing: A small price change could push you over a fee threshold, significantly impacting your net margin. Confirm your category's referral rates and minimums.
  • Reconcile Monthly: Pull a Date Range Report every month. This simple habit helps you catch any fee changes from Amazon early and ensures your ledger remains trustworthy.

Ready-to-Use Beancount Template

To help you get started, I've prepared a starter ledger file. It includes:

  • A sensible Amazon chart of accounts.
  • Inventory configured as commodities for automatic, lot-based COGS.
  • Example entries for sales, fees, storage, refunds, and payouts.

➡️ Download the Template (Open the file in your editor, replace the sample SKU and amounts, and start importing settlement lines.)


References & Further Reading


One Last Tip

If you sell internationally, create marketplace-specific sub-accounts (e.g., Expenses:Marketplace:Amazon:Referral:US, ...:Referral:CA). Set your main operating_currency in Beancount to your home currency. Once your data is structured, Beancount's query language makes it trivial to analyze your fee mix by marketplace, category, or SKU.

Happy booking!

Bookkeeping Basics for Amazon Sellers with Beancount

· 8 min read
Mike Thrift
Mike Thrift
Marketing Manager

When your margins live on pennies, precision beats guesswork.

Selling on Amazon is a game of volume and velocity. But behind the rush of sales and shipments lies a complex web of fees, returns, inventory movements, and tax obligations. Standard bookkeeping software often struggles to capture this nuance, leaving sellers with a fuzzy picture of their true profitability.

2024-07-16-bookkeeping-basics-for-amazon-sellers-with-beancount

This is where a plain-text accounting system like Beancount shines. By giving you total control over how you record transactions, you can build a financial source of truth that perfectly models the unique challenges of the Amazon marketplace. This guide provides a step-by-step workflow to keep you ahead of fees, taxes, and inventory headaches.

Why Amazon Bookkeeping Is Different

If you’ve tried to reconcile an Amazon payout with your bank statement, you already know it's not straightforward. The financial reality of an Amazon business is hidden behind layers of abstraction.

  • Bi-weekly lump-sum payouts: Amazon doesn't send you the revenue from each sale. Instead, it sends a single deposit every two weeks. This lump sum is a net figure, with gross sales reduced by referral fees, FBA fees, advertising costs, returns, and other withholdings. To understand your business, you must break this single number back into its constituent parts. (doola: A Business-in-a-Box™)
  • Inventory everywhere: Your inventory is constantly in motion—from your supplier, to a prep center, to various FBA fulfillment centers across the country, and finally to the customer. Accurately tracking your Cost of Goods Sold (COGS) requires knowing which batch of inventory (at which cost) was used for each sale. (Bean Ninjas)
  • Marketplace fees & promos: A significant portion of your revenue is immediately consumed by fees: referral fees, FBA pick-and-pack fees, monthly storage fees, and advertising costs. Tracking each of these expense categories separately is the only way to calculate your true gross margin and determine a product's real profitability. (Profitwise Accounting)
  • Sales-tax patchwork: While Amazon's Marketplace Facilitator laws handle sales tax collection and remittance in most states, it's not a complete solution. Storing inventory in FBA warehouses can create "nexus" (a business presence), potentially requiring you to register and file in those states, even if no tax is due. This is a complex compliance area that demands careful tracking. (TaxDo)
  • Lower 1099-K thresholds: With the reporting threshold for Form 1099-K dropping from $20,000 to $5,000 in 2024 (and set to fall to just $600 from 2026), nearly every serious seller will receive a form from Amazon reporting their gross transaction volume to the IRS. Your books must be able to reconcile perfectly with this number. (IRS)

Seven-Step Beancount Blueprint

This blueprint leverages Beancount's precision to tackle Amazon's complexity head-on.

1. Separate Channels Early

If you sell on multiple platforms, keep your accounting for each one separate. Within a single Beancount file for your legal entity, create dedicated, hierarchical accounts for each marketplace. This structure simplifies analytics and makes generating tax schedules trivial.

2025-07-22 open Income:Amazon               USD
2025-07-22 open Expenses:Amazon:FBAFee USD
2025-07-22 open Assets:Amazon:Payouts USD

2. Decompose Every Payout

This is the most critical habit. Never book an Amazon deposit as a single line of income. Instead, download the "All Transactions" settlement report from Seller Central for the corresponding period. Use this report to create a single Beancount transaction that breaks the payout into its components.

The deposit you receive in the bank is the balancing entry. The gross sales are credited to Income, while all fees and refunds are debited from their respective Expenses accounts.

; bi-weekly payout from settlement report
2025-07-14 * "Amazon Settlement #4361"
Assets:Bank:Operating 8432.17 USD
Income:Amazon:Sales -12274.50 USD
Expenses:Amazon:FBAFee 2454.80 USD
Expenses:Amazon:Adverts 1012.06 USD
Expenses:Amazon:Refunds 375.47 USD
Assets:Amazon:Reserve -100.00 USD

3. Track Inventory & COGS with Lots

Beancount has a first-class system for tracking inventory called "lots." When you purchase inventory, you record the number of units and their specific cost. When a unit is sold, you can expense that exact cost, giving you a perfect calculation for Cost of Goods Sold (COGS).

; Purchase 1,000 units from a supplier
2025-07-01 * "Supplier PO-7421"
Assets:Inventory:WidgetA 1000 WidgetA {@ 4.20 USD}
Assets:Bank:Operating

; Later, record the cost of a single sale
2025-07-16 * "FBA sale WidgetA | COGS"
Expenses:COGS 1 WidgetA {4.20 USD}
Assets:Inventory:WidgetA

4. Choose Accrual for Clarity

For any inventory-based business, the accrual method is superior. A cash-basis approach would show a massive expense in the month you buy inventory and artificially high profits in the months you sell it, distorting your performance. Accrual accounting correctly matches the cost of the goods sold (COGS) to the revenue from that sale in the same period, providing a much clearer picture of your gross profit. (Bean Ninjas)

5. Automate Imports

Manually entering settlement reports is educational at first, but it doesn't scale. The plain-text ecosystem excels at automation:

  • Use bean-extract to pull data from formatted CSVs exported by services like A2X.
  • Write simple Python scripts to pull data directly from Amazon's SP-API.
  • Use existing importers to pull bank CSV files to reconcile deposits and fees charged directly to credit cards.

6. Reconcile Weekly

Make it a habit to check your numbers. Use Beancount's powerful command-line tools to quickly validate balances and review performance.

# Check your current inventory counts and value
bean-balance books.bean "Assets:Inventory" "2025-07-21"

# Generate an income statement for the last period
bean-report books.bean income_statement -e 2025-07-21

7. Archive Source Docs

For every major transaction, link to the source document. Attach the official Amazon settlement PDF, the supplier invoice for an inventory purchase, or a shipping receipt using Beancount's metadata syntax (document:). This creates a self-contained, audit-ready financial record.

Sales-Tax & Compliance Checklist

  • Marketplace Facilitator Laws: Understand that while Amazon remits sales tax on your behalf in most states, storing inventory in states like California, Texas, or Pennsylvania can still create economic nexus, potentially requiring you to register your business there. (TaxGPT)
  • 1099-K Reconciliation: Ensure that the total you record in Income:Amazon:Sales for the year matches the gross amount reported on your Form 1099-K to the cent. Any discrepancy is an audit flag. (IRS)
  • Direct Sales Tax: If you sell through other channels not covered by a facilitator, maintain a Liabilities:SalesTaxPayable:State account subtree to track taxes you owe directly.

Common Pitfalls (and Fixes)

  • Pitfall: Recording only the net deposit from Amazon.
    • Fix: Always decompose payouts using the full settlement report.
  • Pitfall: Ignoring reimbursed returns or damaged goods.
    • Fix: Log both the initial refund expense and the subsequent reimbursement from Amazon as a separate credit.
  • Pitfall: Forgetting about rolling reserves.
    • Fix: Amazon often withholds a "reserve" balance from payouts, especially for new accounts. Track this money you're owed in a dedicated Assets:Amazon:Reserve account.
  • Pitfall: Mismatching SKU aliases between your system and Amazon's.
    • Fix: Normalize all SKU codes in your import scripts to ensure COGS lookups don't fail.

Quick-Start To-Do

  • Enable and download your first settlement report in Seller Central.
  • Clone a Beancount starter repository and build a chart of accounts specific to Amazon.
  • Write a small importer script that converts a settlement CSV into a Beancount transaction (.txn file).
  • Schedule a weekly reminder to pull new reports and run bean-check to ensure your files are valid.
  • Review your income statement monthly to make data-driven decisions on ad spend, pricing, and inventory.

Further Reading

Ship more, fret less—keep your beans balanced. Happy selling!