Amazon Seller Reconciliation: How to Reconcile Payouts & Fees
Your Amazon bank deposit is a single number. Underneath it sits a tangle of referral fees, FBA charges, returns, advertising spend, and reserve holdbacks. Here is how to untangle it.
The Amazon Seller's Reconciliation Problem
You sold £12,450 worth of products on Amazon this fortnight. Your bank deposit? £8,838.61. The gap is not missing money - it is the sum of every fee, refund, and adjustment Amazon silently deducted before paying you. But unless you can break that single deposit down line by line, your books are incomplete, your margins are invisible, and your VAT return is a guess.
This guide walks through exactly how to reconcile Amazon payouts to your bank statement, with real numbers and a step-by-step process you can follow for every settlement period.
Why Amazon Reconciliation Is So Complex
Most payment processors take a percentage and deposit the rest. Amazon is different. It operates more like a business partner that handles fulfilment, storage, advertising, customer service, and returns on your behalf - then settles up with you every two weeks. The result is a single bank deposit that conceals dozens of different charge types.
The Key Complexity Drivers
- 14-day settlement cycles - Amazon pays sellers fortnightly (and holds reserves for new accounts up to 21 days), so a single deposit can cover hundreds of individual orders
- Multiple fee categories - Referral fees, FBA pick-and-pack fees, monthly storage fees, long-term storage fees, advertising costs, and subscription fees are all deducted before your payout
- Returns offset against payouts - Customer returns, refunds, and A-to-Z Guarantee claims are deducted directly from your next settlement, not processed separately
- Net deposits - Your bank receives one figure: gross sales minus every fee, refund, adjustment, and reserve. Without decomposing it, your accounts show revenue but not true cost of sale
- Cross-period complications - A return processed in settlement period 3 might relate to a sale from settlement period 1, creating timing mismatches
VAT Complication
Amazon charges VAT on its seller fees (referral fees, FBA fees, advertising). These are legitimate input VAT claims, but only if you record them correctly. Booking the net deposit as a single revenue line means you lose the ability to reclaim VAT on thousands of pounds in fees. For a seller doing £25,000/month through FBA, that can easily be £800–£1,200 in reclaimable VAT per quarter.
Anatomy of an Amazon Settlement
Every 14 days, Amazon produces a settlement report in Seller Central. This is your primary reconciliation document. It breaks the payout into granular line items that map to specific accounting categories.
Fee Types You Will See
Referral Fees (7–15%)
Amazon's commission on each sale. The percentage varies by category - electronics typically sit at 7%, while clothing and accessories run at 15%. This is your single largest Amazon cost.
FBA Fulfilment Fees (£2.04–£6.50+ per unit)
The per-unit charge for Amazon to pick, pack, and ship your product. Rates depend on item size and weight. A small standard item under 150g costs £2.04; large oversize items can exceed £6.50.
FBA Storage Fees (£0.70–£3.60 per cubic foot/month)
Monthly charges for warehouse space. Standard rates apply January through September (£0.70/cubic foot). October through December - peak season - rates jump to £1.05 or higher. Long-term storage fees apply to inventory held over 181 days.
Advertising Fees (Sponsored Products, Brands, Display)
If you run Amazon PPC campaigns, your ad spend is deducted directly from your settlement. This often surprises sellers who track advertising in a separate mental bucket - it all comes out of the same payout.
Returns, Refunds, and A-to-Z Claims
Customer refunds are offset against your settlement balance. Amazon also charges a returns processing fee on certain categories. A-to-Z Guarantee claims - where Amazon sides with the buyer in a dispute - are deducted outright.
Worked Example: Breaking Down a Real Payout
Let us walk through a realistic Amazon FBA settlement for a UK seller of home and kitchen products. This covers a standard 14-day settlement period.
Settlement Period: 3–16 February 2026
142 orders shipped via FBA. 8 returns processed. 1 A-to-Z claim resolved in the buyer's favour.
| Item | Amount |
|---|---|
| Gross Sales (142 orders) | £12,450.00 |
| Referral Fees (15% avg.) | −£1,867.50 |
| FBA Fulfilment Fees | −£892.30 |
| FBA Storage Fees | −£45.20 |
| Sponsored Products Ad Spend | −£340.00 |
| Returns & Refunds (8 items) | −£376.40 |
| A-to-Z Guarantee Claim (1) | −£89.99 |
| Bank Deposit | £8,838.61 |
That £8,838.61 is what hits your bank account. If you book it as a single revenue entry, you are overstating net revenue (it contains fee deductions) and missing £3,611.39 in expense categorisation. Your profit and loss statement will show the wrong gross margin, your cost of sales will be understated, and you will miss VAT recovery on fees where Amazon charged you VAT.
The Margin Visibility Problem
In our example, the seller's effective Amazon take rate is 29.0% (£3,611.39 in total deductions against £12,450 gross). But without breaking the settlement down, they cannot see that referral fees alone consume 15%, fulfilment costs another 7.2%, and advertising is 2.7%. These ratios matter when deciding whether to adjust pricing, switch to Merchant Fulfilled (MFN), or reallocate ad budget.
Proper reconciliation is not just about balanced books - it is about understanding which Amazon costs are eating your margin.
Step-by-Step Amazon Reconciliation Process
Download Your Settlement Report
In Seller Central, go to Payments > All Statements. Select the settlement period and download the report as a CSV or TSV. This contains every transaction, fee, refund, and adjustment for that cycle. For more granular data, use the Date Range Reports under Payments > Reports to pull transaction-level detail.
Export Your Bank Statement
Download a CSV or PDF of your bank statement covering the settlement deposit date. Look for the deposit from “AMAZON PAYMENTS” or “AMAZON EU S.A R.L.” - the reference will usually include a settlement ID. If you receive deposits from multiple Amazon marketplaces (UK, DE, FR), each will appear as a separate settlement.
Map Settlement Items to Accounting Categories
Group the settlement line items into accounting categories: revenue (gross product sales), cost of sales (referral fees, FBA fulfilment), overheads (storage, subscription), marketing (advertising spend), and adjustments (returns, claims). Each category posts to a different nominal account in your chart of accounts.
Match the Net Deposit to Your Bank
Verify that the settlement report total matches the bank deposit exactly. If there is a discrepancy, check for reserve holdbacks (Amazon holds a percentage for new or flagged accounts), currency conversion adjustments on European marketplace sales, or subscription fees that were charged to the settlement rather than your card.
Post Fees to the Correct Expense Accounts
Enter each fee category as a separate transaction in your accounting software. Post gross revenue as income, referral fees to selling expenses, FBA fees to distribution costs, storage to warehousing, advertising to marketing, and refunds as contra-revenue or a dedicated returns account. This gives you a clean P&L with accurate Amazon channel margins.
Common Traps and How to Avoid Them
Trap 1: Booking the Net Deposit as Revenue
The most common mistake. If you record £8,838.61 as sales revenue, you are understating your actual sales by £3,611.39 and hiding all your Amazon costs. Your gross margin will look artificially high because the expenses are invisible. Always record gross sales and fees separately.
Trap 2: Ignoring Cross-Period Returns
A customer returns a product they bought in January during a February settlement cycle. The refund appears in the February settlement, reducing your February payout. If you only look at February sales minus February deposits, the numbers will not add up. Track returns against the original sale period for accurate monthly revenue reporting.
Trap 3: Missing VAT on Amazon Fees
Amazon charges VAT on referral fees, FBA fees, storage fees, and advertising. These appear on your Amazon VAT invoices (Settings > Account Info > VAT invoices). If you do not claim this input VAT, you are effectively paying 20% more for every Amazon service than you need to. For our example seller, the reclaimable VAT on fees is approximately £525 per settlement period.
Trap 4: Confusing Reserves with Missing Money
Amazon holds a reserve on new accounts, accounts with high claim rates, or during peak seasons. This reserve is deducted from your settlement but released in a future period. It is not a fee - it is a timing difference. Record it as a receivable (money Amazon owes you) rather than an expense. When it is released, it will appear as an addition in a later settlement.
Automating Amazon Reconciliation
Manually decomposing settlement reports works for sellers processing a handful of orders. Once you scale past 100 orders per settlement - or sell across multiple Amazon marketplaces - the manual approach breaks down. Each settlement can contain 500+ line items when you count individual fees and adjustments per order.
ReconcileIQ for Settlement Matching
Upload your Amazon settlement report and bank statement as CSVs. ReconcileIQ matches the net settlement total to the corresponding bank deposit, flags discrepancies from reserves or currency adjustments, and handles the many-to-one matching where a single bank deposit maps to hundreds of underlying transactions.
For sellers on multiple marketplaces, it can reconcile UK, DE, FR, IT, and ES settlements against the respective bank deposits in a single pass - handling cross-currency conversions automatically.
CodeIQ for Ongoing Amazon Bookkeeping
Where ReconcileIQ matches settlements to bank deposits, CodeIQ handles the ongoing categorisation. It learns that “AMAZON EU S.A R.L.” bank deposits should be coded to your Amazon revenue account, identifies FBA fee patterns, and auto-codes advertising charges to marketing expenses.
Over time, it builds a pattern library specific to your Amazon business - recognising storage fee spikes in Q4, distinguishing between regular settlements and reserve releases, and applying the correct VAT treatment. What used to take an hour of manual posting per settlement becomes a two-minute review.
The combination addresses both sides of the Amazon reconciliation problem: confirming that the right money arrived in your bank (ReconcileIQ), and making sure every component is posted to the right account in your books (CodeIQ).
Simplify Your Amazon Reconciliation
Stop booking net deposits as single lines. Break down every Amazon fee, reclaim your VAT, and see your true channel margins.
Try ReconcileIQ FreeFrequently Asked Questions
How do I reconcile Amazon seller payouts with my bank statement?
Download your Amazon Settlement Report from Seller Central (Payments > All Statements), then export your bank statement for the same settlement period. The net deposit in your bank should equal gross sales minus all Amazon fees, returns, refunds, and adjustments shown in the settlement report. Match the single bank deposit to the settlement total, then post each fee category to the correct expense account.
Why doesn't my Amazon payout match my sales total?
Amazon deducts referral fees (typically 7–15%), FBA fulfilment fees, storage fees, advertising costs, returns, refunds, and A-to-Z Guarantee claims before depositing funds. A settlement covering £12,450 in gross sales might result in a bank deposit of only £8,838 after all deductions. The settlement report in Seller Central breaks down every deduction.
What is the best tool for Amazon seller reconciliation?
ReconcileIQ can match Amazon settlement reports against bank deposits, handling the net-of-fees reconciliation automatically. For ongoing bookkeeping, CodeIQ learns your Amazon transaction patterns and auto-codes each fee type to the correct expense account, eliminating manual categorisation of FBA fees, referral fees, advertising spend, and refunds.
How do I account for Amazon FBA fees in my bookkeeping?
FBA fees should be posted to a dedicated expense account such as “Amazon FBA Fulfilment Fees” or “Distribution Costs”. Record gross revenue at the full sale price, then post each fee type separately: referral fees to selling expenses, FBA fees to fulfilment costs, storage fees to warehousing expenses, and advertising spend to marketing costs. This gives you accurate margin visibility per channel.