FBA Fee Audit: the Five Lines to Check on Every SKU

Why five lines and not one

Most sellers who audit fees at all check one line — usually the fulfillment fee, because it's the most visible and the one most guides write about. That leaves four other lines unchecked, and in our experience the dollar value doesn't reliably concentrate in the fulfillment fee specifically; it tends to sit in whichever line hasn't been looked at recently, on whichever SKU changed most recently. A five-line check costs marginally more time than a one-line check and finds a materially larger share of what's actually recoverable, which is the entire argument for treating this as a checklist rather than a single number to glance at.

Line one: the referral fee percentage

Referral fees range from about 5% to 45% of the sale price depending on category, with most categories carrying a $0.30 minimum per item, and several categories charge in tiers within themselves rather than one flat percentage — watches, for instance, are charged 16% on the portion of the sale price up to $1,500 and 3% on anything above that, and some beauty products are charged 8% at or below $10 and 15% above it. The audit check here isn't “is my referral fee roughly right” — it's confirming the exact category assignment and, for any tiered category, that the correct band is being applied to the correct portion of the price. A SKU that's drifted into the wrong category classification can be over- or under-charged on every single sale.

Line two: the fulfillment fee's size tier

Covered in depth elsewhere on dimensional weight and tier drift specifically, but the audit-line version is simple: measure the actual shipped, sealed package and confirm the size tier Amazon has on file matches it. This is the line most likely to have drifted silently, because nothing prompts a re-check when packaging changes on the supplier side.

Line three: monthly storage fees

Storage is charged per cubic foot, monthly, and the rate is higher in the October-through-December peak months than the rest of the year — check that the size-tier cubic footage being billed matches your actual product, and that a seasonal rate change hasn't been missed in a spreadsheet that only gets updated once a year. Storage fee errors are usually smaller per unit than fulfillment-fee errors, but they apply to every unit sitting in inventory, sold or not, which makes overstocked SKUs disproportionately exposed here.

Line four: the aged-inventory surcharge

This is the line most frequently misquoted across the industry, including in our own earlier materials before correction, because the exact day-thresholds and dollar amounts change periodically and a lot of published guidance is stale. Rather than repeat a number that may already be out of date by the time you're reading this, the audit check is structural: confirm your aged-inventory report matches your actual understanding of what's been sitting unsold, and check the current thresholds directly on Amazon's own pricing page before assuming last year's numbers still apply. A SKU with slow turnover that crosses an aged threshold unnoticed accrues a surcharge that keeps compounding, similar in shape to a size-tier drift but calendar-driven rather than packaging-driven.

Line five: open reimbursement gaps from the last 90 to 120 days

This line ties the fee audit back to the reimbursement side rather than treating them as separate problems, because a fee audit that finds a genuine overcharge and a reimbursement audit that finds a lost unit are the same kind of check run against different data: comparing what should have happened against what your settlement records actually show. Specifically: any refund issued in the last 60 to 120 days without a matching returned unit, and any fulfillment-center loss reported in the last 60 days without a matching reimbursement credit, both belong on this list — they're the fee audit's closest cousin, and running them together avoids duplicating the reconciliation work across two separate processes.

Practically, this means pulling the same underlying reports described on our reimbursement-audit page and reconciling them in the same sitting as the first four lines, rather than as a separate exercise on a separate day. The report joins are largely the same regardless of which of the five lines you're checking, so running them together is close to free once the first line's reconciliation work is already done.

A worked example of what five lines finds that one line misses

In one account, a transaction-level pass across just the inbound-shipping portion of these five lines — not even the full set — found roughly $65,000 of incorrect deductions across two months, invisible at the settlement-summary level because no single error was large enough to stand out on its own. That's the case for running all five lines rather than spot-checking whichever one seems most likely to be wrong: the dollar value tends to concentrate in whichever line hasn't been checked recently, not in the same line every time.

Worth naming separately: an audit that finds a discrepancy has to check which direction it runs before acting on it. In a different account, a client asked us to dispute what looked like an overcharged fulfillment fee, and the transaction-level check found Amazon was actually undercharging on nine of the products in question — filing that dispute would likely have raised the fee, not lowered it. We advised against filing. An audit that only ever reports discrepancies in the client's favor isn't a complete audit; it's a one-sided one, and it will eventually recommend a dispute that backfires.

Making the five-line check a habit, not a project

Full Circle has managed more than $500M in Amazon spend across 100+ brands, and running these five lines on a consistent cadence — weekly on the highest-volume SKUs, monthly across the rest of the catalog — is what actually finds money before it compounds into a large, hard-to-explain gap. Dr. Shield runs this as a standing audit rather than a one-time project, priced on the call as a contingency against what's found and recovered, because a fee audit done once a year finds last year's problem, not this quarter's.