Understanding Amazon FBA Fees: A Bookkeeper's Guide

The Challenge of Amazon FBA Fee Accounting

Amazon FBA sellers face a dizzying array of fees that appear in their settlement reports. As a bookkeeper, understanding these fees is essential for accurate financial reporting. This guide breaks down every major fee category, explains how it appears in the settlement data, and recommends how to categorize it in your chart of accounts.

Referral Fees (Commission)

Amazon charges a referral fee on every sale, calculated as a percentage of the total sale price (including shipping). The rate varies by product category, typically ranging from 6% to 45%, with most categories at 15%.

In the settlement report, referral fees appear as: - Amount Type: ItemFees - Amount Description: Commission - Sign: Negative (deduction from your balance)

Accounting treatment: Debit to "Amazon Referral Fees" or "Marketplace Commission Expense"

When a customer receives a refund, Amazon refunds a portion of the referral fee back to you. This appears as RefundCommission and should be credited against your referral fees expense.

FBA Fulfillment Fees

These are the pick, pack, and ship fees Amazon charges for handling your inventory. The amount depends on the item's size tier and weight.

Common fulfillment fee descriptions in the settlement: - FBAPerUnitFulfillmentFee — standard per-unit fee - FBAPerOrderFulfillmentFee — per-order handling fee - FBAWeightBasedFee — additional fee for heavy items

Accounting treatment: Debit to "FBA Fulfillment Fees" or "Fulfillment Expense"

These fees represent a significant cost for most FBA sellers, often 20-30% of the product price for small, lightweight items.

Storage Fees

Amazon charges monthly storage fees based on the cubic feet of space your inventory occupies in their warehouses.

• Monthly storage fees appear as FBAInventoryStorageFee
• Long-term storage fees (for inventory stored over 181 days) appear as FBALongTermStorageFee

Long-term storage fees are significantly higher and can devastate margins on slow-moving inventory.

Accounting treatment: Debit to "FBA Storage Fees" — consider breaking out long-term storage as a separate line item for visibility.

Shipping Chargebacks

When the buyer-paid shipping doesn't cover Amazon's actual shipping cost (common for heavy or oversized items), the difference appears as a shipping chargeback.

• Amount Description: ShippingChargeback

Accounting treatment: Debit to "Shipping Chargebacks" or group with fulfillment fees.

Variable Closing Fees

Applicable to media categories (books, music, DVDs), this is a flat fee per item sold.

• Amount Description: VariableClosingFee

Accounting treatment: Debit to "Amazon Variable Closing Fees" or group with referral fees.

Advertising Fees

If you run Sponsored Products, Sponsored Brands, or Sponsored Display campaigns, the ad spend may appear in your settlement.

• Amount Description: CostOfAdvertising

Accounting treatment: Debit to "Amazon Advertising Expense" — keep this separate from marketplace fees for accurate ROAS tracking.

Subscription Fees

The Professional selling plan costs $39.99/month. This appears in one settlement per month.

• Amount Description: Subscription Fee

Accounting treatment: Debit to "Amazon Subscription Fee" or "Software Subscriptions"

FBA Removal and Disposal Fees

When you request inventory removal or disposal: - FBARemovalFee — fee for returning inventory to you - FBADisposalFee — fee for Amazon to destroy unsellable inventory

Accounting treatment: Debit to "FBA Removal/Disposal Fees" — useful to track for inventory management decisions.

Inbound Placement Fees

Amazon's newer fee for distributing inventory across multiple fulfillment centers.

• Amount Description: FBAInventoryPlacementServiceFee

Accounting treatment: Debit to "FBA Inbound Placement Fees"

Marketplace Facilitator Tax

In states where Amazon is the marketplace facilitator, they collect and remit sales tax on your behalf. These amounts flow through the settlement as withholdings.

• Amount Type: ItemWithheldTax
• Descriptions: MarketplaceFacilitatorTax-Principal, MarketplaceFacilitatorTax-Shipping

Accounting treatment: These are pass-through amounts. Debit and credit cancel out in your journal entry since Amazon collects and remits the tax. Track them for reconciliation but they don't affect your P&L.

Chart of Accounts Recommendations

For most FBA sellers, we recommend these accounts:

Account	Type	Notes
Product Sales	Revenue	All ItemPrice/Principal amounts
Shipping Revenue	Revenue	ItemPrice/Shipping
Amazon Referral Fees	Expense	Commission + RefundCommission
FBA Fulfillment Fees	Expense	All fulfillment-related fees
FBA Storage Fees	Expense	Monthly + long-term storage
Refunds Issued	Contra-Revenue	Refund/Principal + Refund/Shipping
Promotions & Discounts	Contra-Revenue	Promotion/Principal
Amazon Advertising	Expense	CostOfAdvertising
Other Amazon Fees	Expense	Catch-all for new/uncommon fees

Handling Unknown Fee Types

Amazon periodically introduces new fee types. When your bookkeeping tool encounters an unrecognized fee code, it should:

1. Map it to a catch-all "Other Amazon Charges" account
2. Flag it for review
3. Allow you to create a custom mapping for future settlements

This is exactly how SettleBooks handles unknown fees — nothing gets silently dropped, and you can customize the categorization to match your chart of accounts.

Key Takeaways

• Amazon FBA has 15+ distinct fee types that require proper categorization
• Referral fees and fulfillment fees are the largest expense categories for most sellers
• Always track refund-related fee credits separately — they offset your expenses
• Set up your chart of accounts with enough granularity to identify cost drivers
• Use consistent categorization across settlement periods for meaningful trend analysis