Reconciling an Amazon FBA account is not a mysterious process. It is a comparison: what you sent Amazon and what Amazon says it has, set against each other per FNSKU, with the difference explained. The work that decides whether that comparison is any good happens before it starts, in the exports you pull out of Seller Central.

This guide covers which reports to export, how to keep the exports clean, what to have ready that no report contains, and what the comparison can and cannot tell you afterwards. It is written for a seller doing it themselves, whether that is in a spreadsheet or in Leviathan Recon, which rebuilds the unit ledger from these same files.

Start with four reports

You do not need your whole reporting history to see something useful. Four exports are enough to start, and between them they reveal inbound shortages:

Shipped to FBA
Inventory Event Detail
Reimbursements
Inbound Shipments

Those four cover the most common gap in an FBA account: units that left your supplier or warehouse, arrived at a fulfillment center, and were never checked in against the shipment that carried them. If you export nothing else this month, export these.

Then the rest, as you need them

Recon ingests sixteen report types in total, and the modules that read them cover shipments, removals, returns, replacements, FC transfers, Grade & Resell, adjustments and full inventory. Each module wants its own slice of Seller Central, so the set you export grows with the questions you are asking. If returns are where your losses are, the returns reports matter more than the removal reports.

Fifteen of those sixteen have a downloadable CSV template, so you can see the columns the upload expects before you go looking for the report. The settlement report is the exception: it has no template, because its shape comes from Amazon rather than from us. For what settlement data is good for once you have it, our guide to settlement reconciliation covers the finance side of the same problem.

Keeping the exports clean

Most reconciliation problems are export problems wearing a disguise. Four habits prevent nearly all of them.

Pull whole periods, not convenient ones. A report that starts mid-month cuts shipments in half, and a shipment split across two exports reconciles against nothing. Match your export windows to the period you intend to review, then extend the inbound reports a month further back: a shipment closes long after it ships.

Keep one marketplace to a workspace. Blending Amazon.com and Amazon.ca rows into one pile produces variances that are really currency and marketplace differences. Recon supports sellers on Amazon US, Canada and India; keep each one's reports separate when you export them.

Do not tidy the file. Opening a CSV in a spreadsheet to delete a column, reformat a date or strip a currency symbol is the single most effective way to make a good export unreadable. Download it, leave it, upload it.

Re-export rather than patch. If a report looks wrong, pull it again. Duplicate rows are detected by hash and skipped, so a re-upload of a file you have already sent adds nothing to the ledger. That is deliberate, and it means uploading again is the cheap move when you are unsure which copy was right.

What no report contains

Two things decide what a discrepancy is worth, and neither of them is in any export.

Your per-unit cost. Since March 2025 Amazon reimburses lost and damaged FBA inventory at your manufacturing or sourcing cost rather than the sale price, and where the cost field in Seller Central is missing or zero, Amazon substitutes its own estimate. Verifying that field for every active SKU is the highest-value preparation you can do, and it pays on every future claim, not just this month's. Our 2026 reimbursement policy guide covers the mechanics.

The evidence behind the number. Commercial invoices, bills of materials, supplier payment records, carton manifests, proof of delivery, carrier signatures. Recon rebuilds your unit ledger and shows you where it disagrees with Amazon's balance; it does not produce cost documentation, and it does not assemble a claim. Keeping those records filed by shipment, dated and where you can find them again, is your side of the work.

While you are in cost-data mode, our FBA calculator is a quick way to check that a SKU's landed cost still clears a sensible margin at the current fee schedule.

What the comparison shows you

Once the files are uploaded, the reconciliation runs per FNSKU, not per MSKU or ASIN, and every FNSKU comes back with a status you read on your own screen:

Reconciled for the ones where your ledger and Amazon's balance agree.
Over where Amazon shows more than your ledger accounts for.
Reimbursed where a discrepancy has already been paid.
Take Action where there is a variance you may want to raise with Amazon.
No Snapshot where there is not enough data to say.

Behind each figure, the Data Explorer keeps fifteen raw tables searchable, filterable and exportable to CSV, so a variance is something you check rather than something you take on trust. The Action Center is where you track the cases and adjustments you raise, per module, with status, remarks and attachments.

What happens next is yours. You open a Take Action row, look at the units behind it, and raise the case in Seller Central yourself. Recon does not file claims and cannot act in your account: it reads the files you upload, and nothing else.

One limitation worth knowing before you start

Reimbursements for lost inbound units key on FNSKU alone. If a single FNSKU is spread across several shipments, those shipments share one reimbursement pool, and the reconciliation cannot attribute a given reimbursement to the specific shipment it belongs to. Where that matters to you, your own shipment records are what settle it.

This is worth saying plainly, because it is the kind of thing a tool is tempted to paper over. A reconciliation narrows the question and shows you the rows underneath it. It does not close every question by itself.

If other people will help

Access inside a workspace is Recon's own, not Amazon's: each user your admin creates is an Admin, a Vendor or a Viewer, permissions can be set per user and per module on top of that, and every change is written to an audit log. Your bookkeeper can work the returns side without touching anything else, and you can see afterwards what they changed.

Prepare once, then run it monthly

Most Amazon reimbursement claim windows are around 60 days, and the exact window depends on the case type. That makes reconciliation a rhythm rather than a project. The preparation above is mostly one-time: cost fields verified, evidence filed where you can find it, export windows that line up. After that, each month is the same four to sixteen exports and a list of Take Action rows to work through.

Start the 14-day free trial of Leviathan Recon when your exports are ready. There is no card on file, no API connection to your account and no credential of yours for Recon to hold: you upload the files, and Recon rebuilds your unit ledger from them.