How to Reconcile Your Amazon Settlement Report (Step-by-Step)
12 min read
Reconciling an Amazon settlement report by hand is entirely possible at low volume — the process below is the same logic a dedicated reconciliation tool automates, just done manually in a spreadsheet.
What you're actually trying to prove
Reconciling an Amazon settlement report means proving, order by order, that every unit you shipped appears in a settlement, that the fees deducted match what should have applied, and that nothing was charged twice or omitted. The end state isn't a single number — it's a list of exceptions: orders that don't match, and exactly how they don't match.
This only works if you have two independent sources of truth to compare against each other: your own order records (what you shipped, at what price, in what category) and Amazon's settlement data (what it actually paid you and deducted). Reconciling a settlement report against itself — just re-adding its own numbers — only catches arithmetic errors, not the more common category of error where the wrong fee was applied to a real transaction.
Step 1: Download the right reports
From Seller Central, go to Reports > Payments > All Statements (or Payments > Transaction View for a more granular row-by-row export) and download the settlement/payments report for the cycle you're reconciling — Amazon typically settles on a rolling cycle, commonly every 14 days for standard sellers. Separately, download your order report (Reports > Fulfillment by Amazon, or the general Orders report) for the same date range, since this is the independent 'what actually shipped' source.
If you need to verify TDS/TCS specifically, Reports > Tax Reports has a consolidated TDS/TCS view that's faster to cross-check than pulling the figures out of individual transaction rows.
Step 2: Build a common key to match rows
Both reports need a shared identifier to join on — usually the Order ID, sometimes combined with a transaction type (Order, Refund, Adjustment, Service Fee) since a single Order ID can appear multiple times in the settlement report if it was later returned or adjusted. In a spreadsheet, this typically means a helper column that concatenates Order ID and transaction type, used as the lookup key for XLOOKUP or a Power Query merge between the two report tabs.
This step is where manual reconciliation most commonly breaks down at scale: partial shipments, multi-unit orders split across settlement lines, and orders that span two settlement cycles all produce Order IDs that don't map cleanly 1:1 between the two files. At low volume this is a manageable, occasional cleanup task; at higher volume it becomes the majority of the actual reconciliation effort.
Step 3: Check that every shipped order actually appears in the settlement
Using the matched key, identify any Order ID present in your order report but absent from the settlement report entirely for the period. This is the most financially significant check to run first, since a missing settlement means Amazon hasn't paid for that order at all — not underpaid, unpaid.
A missing order isn't automatically an error — it may simply not have reached its scheduled settlement date yet, or it may be part of a delayed or held payment. But if an order was shipped well outside the normal settlement cycle length and still hasn't appeared, that's a strong candidate to investigate directly with Seller Central support before too much time passes.
Step 4: Verify the referral fee (commission) percentage for each order
For each matched order, calculate what the referral fee should be — item price × the referral fee percentage for that product's actual category — and compare it against the referral fee actually deducted in the settlement row. Amazon's referral fee varies by category, roughly in the low single digits for some categories up to over 20% for others, so this check requires knowing (or maintaining a reference table of) the correct rate per category, not a single flat percentage.
A mismatch here usually traces to one of two causes: the product is filed under the wrong category in Amazon's catalog, so the wrong referral fee rate applies to every order of that SKU until the listing is recategorized; or a promotional/reduced referral fee rate that should have applied to a specific order (some categories or programs carry temporary reduced rates) wasn't actually applied.
Step 5: Verify FBA or Easy Ship fulfillment fees
Fulfillment fees are driven by size tier and weight, so the check here isn't a flat percentage — it's confirming the product's actual dimensional weight and size tier map to the fee tier that was actually charged. A product that should sit in a smaller size tier but is being billed at a larger tier's rate (due to inaccurate dimension data on file, or a packaging change that was never updated in Seller Central) will overcharge on every single unit sold, not just one order.
This is also where storage fees, long-term storage surcharges, and removal fees show up if applicable — these are separate line items from the per-order fulfillment fee and are worth reconciling against the Recommended Removal and Inventory reports rather than the settlement report alone.
Step 6: Reconcile returns and refunds against reimbursements
For every order that was returned, confirm three things line up: the refund issued to the customer matches the order value (not more, not less), any return-shipping or restocking fee was applied correctly, and — critically — check whether a corresponding reimbursement is owed if the returned item was lost, damaged, or never actually came back to a fulfillment center. This last check is the one most manual reconciliations skip entirely, because it requires cross-referencing the Reimbursements report separately rather than just accepting the refund line at face value.
A returned order that shows a refund debit but no matching reimbursement credit, where the return tracking shows the item was never actually delivered back to Amazon, is a SAFE-T claim candidate — worth filing separately rather than writing off as an ordinary return.
Step 7: Verify TDS (194-O) and TCS (Section 52) deductions
TDS under Section 194-O is currently 0.1% of gross sale value (reduced from 1% effective 1 October 2024), and GST TCS under Section 52 is currently 0.5% of net taxable value (reduced from 1% effective 10 July 2024). Calculate both directly from each order's figures and compare against the deducted amounts in the settlement report — a mismatch here isn't just a payout issue, it's a tax-credit issue, since these figures need to eventually tie back to Form 26AS (for TDS) and GSTR-2B (for TCS).
Because these rates changed partway through recent financial years, the most common false-positive in this step is applying the old rate to a transaction that actually falls after the rate-change date, or vice versa — always check the transaction date against the effective date before flagging a mismatch as an error.
Step 8: Total the exceptions, not just the totals
The output of a proper reconciliation isn't a single reconciled total — it's a list of every order where something didn't match, tagged by which check it failed (missing settlement, referral fee mismatch, fulfillment fee mismatch, refund/reimbursement mismatch, TDS/TCS mismatch). That list is what actually gets acted on: disputed with Seller Central, filed as a SAFE-T claim, or corrected at the listing/category level so it stops recurring.
A grand total that 'looks about right' can hide a mix of overcharges and undercharges that cancel each other out in the aggregate while still representing real, individually recoverable errors — which is exactly why order-level exception lists matter more than a reconciled summary number.
Where manual reconciliation stops scaling
Every step above is genuinely doable in a spreadsheet, and plenty of sellers do exactly this at low order volume. What breaks down as volume grows isn't any single step being hard — it's that all eight steps need to run every settlement cycle, correctly, before each category of error's dispute window closes, across potentially thousands of line items with category-specific rate tables that change without notice.
TheEcomWay's reconciliation engine runs this same eight-step logic automatically against your uploaded Amazon settlement and order reports — including current referral fee rates by category, size-tier fulfillment fee checks, TDS/TCS rate verification, and reimbursement cross-referencing — and returns only the exceptions, in under 30 seconds, every cycle.
Frequently Asked Questions
What two reports do I need to reconcile an Amazon settlement?
Your own order report (what you actually shipped, at what price and category) and Amazon's settlement/payments report (what was actually paid and deducted), for the same date range. Reconciling the settlement report against itself only catches arithmetic errors, not incorrect fees applied to real transactions.
What's the single most financially important check to run first?
Confirming every order in your own records actually appears in the settlement report at all. A missing settlement means an order hasn't been paid for yet — not underpaid, unpaid — which is a bigger gap than a fee-percentage mismatch on an order that did settle.
Why would the same product show a different referral fee on different orders?
Usually a category misclassification in the catalog, which applies the wrong referral fee rate to every order of that SKU, or a promotional/reduced rate that should have applied to a specific order but wasn't picked up. Both require checking the applied rate against the current official rate for the product's actual category.
How do I check if a returned order should have triggered a reimbursement?
Cross-reference the return against the Reimbursements report and the return's tracking status. If the tracking shows the item was never actually delivered back to a fulfillment center but the customer was still refunded, that's a SAFE-T claim candidate, not just an ordinary return to write off.
What are the current TDS and TCS rates I should check against?
TDS under Section 194-O is 0.1% of gross sale value (reduced from 1% effective 1 October 2024). GST TCS under Section 52 is 0.5% of net taxable value (reduced from 1% effective 10 July 2024). Always check the transaction date against these effective dates before flagging a mismatch, since applying the old rate to a post-change transaction is the most common false alarm.
Can I reconcile Amazon settlements manually at any order volume?
Yes at low volume — a few hundred orders a month with simple category mixes is manageable in a spreadsheet. It becomes impractical at higher volume because all the checks need to run every settlement cycle, correctly, before dispute windows close, across category-specific rate tables that change without notice.