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Amazon FBA Bookkeeping: How to Track Inventory and Sales

Published April 2026

Amazon FBA (Fulfillment by Amazon) simplifies logistics for sellers but complicates bookkeeping. Between referral fees, storage charges, and complex cost structures, many FBA sellers struggle to understand their actual profit margins. Proper bookkeeping reveals which products are truly profitable.

Understand Your FBA Fee Structure

Amazon charges a referral fee on nearly every product sold. For most categories, this is 15% of the sale price. You also pay FBA fulfillment fees based on the size and weight of your item, typically ranging from $2 to $15 per unit. Additionally, storage fees apply monthly for units in Amazon warehouses at approximately $0.87 per cubic foot for standard-size items and $0.52 per cubic foot for oversize items.

Track Inventory Costs Accurately

Every dollar spent sourcing products is a deductible business expense. Document your unit cost, quantity purchased, and date for all inventory. If you use multiple suppliers, separate these costs by supplier so you can identify your best margins. Use your Seller Central inventory reports to track quantity on hand and match it against your accounting records monthly.

Monitor Storage Fees Monthly

Storage fees are a major profit killer if you don't manage them. Create a calendar reminder to check your monthly FBA storage charges and compare them against your historical data. If storage fees are consuming 10% or more of your revenue, you need to adjust pricing, reduce stock levels, or remove slow-moving inventory.

Reconcile Amazon Payouts to Your Bank Account

Amazon deposits your net earnings (after all fees) into your designated bank account on a set schedule. Your Seller Central account shows pending funds, completed orders, and deductions. Your bank shows actual deposits. These sometimes don't match immediately due to timing, refunds, or chargebacks. Reconcile weekly to catch discrepancies early.

Account for Returns and Refunds

Amazon deducts refunds from your proceeds directly. When a customer returns an item, Amazon processes the refund and you lose the referral fees paid on that sale. Track return rates by product to identify quality issues or inaccurate product descriptions that drive excessive returns.

Separate FBA and Non-FBA Sales

If you sell both FBA and Merchant Fulfilled items, keep these revenue streams separate in your bookkeeping. FBA has a completely different fee structure than Merchant Fulfilled. Tracking separately shows which fulfillment method is more profitable for your business.

Calculate True Product Profitability

To know if a product is actually profitable, you need to calculate: product cost plus all Amazon fees plus any additional costs (advertising, packaging, returns processing). Only then can you see your true margin. Many FBA sellers discover that their best-selling product is actually unprofitable once you include all fees.

Plan for Quarterly Taxes

As an FBA seller, you are typically considered self-employed and owe quarterly estimated taxes. Calculate your net profit (revenue minus all costs and fees), and plan to set aside 25-30% for taxes. Keep detailed records of all deductions: sourcing costs, storage, referral fees, and advertising spend.

FBA bookkeeping requires discipline and regular reconciliation, but it is worth it. Understanding your true cost structure lets you make smart decisions about pricing, inventory management, and business growth.