The Complete Guide to Amazon Reimbursement Audits

If you sell to Amazon through Vendor Central, a reimbursement audit is not an optional "cleanup" task. It is a vital financial control. In 2026, Amazon’s automated deduction engine has reached peak efficiency, while their recovery windows have reached peak strictness.

A systematic audit identifies, validates, and recovers money that Amazon has deducted incorrectly. For most accounts, this process recovers 2% to 5% of annual gross revenue.

Phase 1: The Forensic Data Pull

You cannot audit what you cannot see. Accuracy at this stage determines your total recovery potential. You must centralize three data types:

Phase 2: The Audit Workflow (8 Key Steps)

1. Shortage Reconciliation (The "Heavy Hitter")

The audit compares Units Invoiced against Units Received.

• The Check: Validate every "shortage" against the POD and carrier signature.

• 2026 Warning: Amazon now relies on automated gate-scans. If the scan is wrong, the shortage is "permanent" unless you produce the signed BOL immediately.

2. Damaged & Lost Inventory Audit

Inventory marked as "Warehouse Damaged" must be converted into a financial credit.

• The Check: Verify that every damaged unit has a corresponding "Approved" status and a unique Remittance Credit ID.

• The Leak: Often, cases are "Approved" in the system but never actually paid out in a remittance.

3. Chargeback Forensic Analysis

Not all chargebacks are valid. Many are triggered by system glitches or "Phantom Late ASNs."

• The Check: Categorize chargebacks by code (e.g., Code 20: ASN, Code 30: Packaging). Identify repeat offenders (e.g., specific Fulfillment Centers) to prove a systemic error on Amazon's side.

4. Returns & Restock Validation

This ensures that when Amazon deducts for a customer return, you actually got the stock back (or the money).

• The Check: Reconcile "Return Authorizations" against "Physical Receipt" at your warehouse.

• The Leak: Units deducted as "Damaged Return" that were actually sellable inventory.

5. Price Claim Audits

Amazon often applies "Price Protection" or "Co-op" deductions based on outdated agreements.

• The Check: Compare the Invoice Unit Price against the PO Unit Price.

• The Fix: Flag any discrepancy where Amazon paid the "current" price for stock that was ordered under a "previous" (higher) price agreement.

6. Duplicate Deduction Detection

High-volume accounts often suffer from "Double Dipping"—where one error triggers two different deductions (e.g., a shortage and a related compliance fee).

• The Check: Search for identical financial values across different deduction codes within the same 30-day window.

  
  

7. The Dispute Filing System

Identifying the error is 50% of the work. Submission is the other 50%.

• The Standard: Every dispute must include:

  • The Original PO & Invoice

  • Signed Proof of Delivery (POD)

  • The specific Deduction/Credit Memo ID

• Tip: Amazon’s 2026 AI-led dispute review will auto-reject any filing that lacks a machine-readable POD.

8. Remittance Matching (The Final Mile)

The audit is not finished when the claim is "Approved." It is finished when the money is in your bank.

• The Check: Tie every "Approved Case ID" to a specific line on a Settlement Report.

Ongoing Monitoring vs. One-Off Projects

In 2026, "Annual Audits" are obsolete. With dispute windows narrowing to 30–60 days for many categories, a one-off audit will leave 80% of your money on the table.

Pro Tip: Transition to a "Rolling Audit." Reconcile every Friday. If you wait until the end of the quarter, the "Dispute" button on Vendor Central may already be greyed out.

CFO Impact Summary: £5M Account Example

• Recoverable Leakage (3%): £150,000

• Time to Cash: 45 to 90 Days

• Required Effort: High (Manual) / Low (Automated)

Unlike marketing or R&D, reimbursement recovery has a 1:1 impact on Net Profit. Every £1 recovered is £1 of profit.

Frequently Asked Questions

• How far back can we audit?
  Generally, 2 years for shortages, but as little as 30 days for certain operational chargebacks.

• Why is my "Approved" claim still unpaid?
  Approvals often sit in a "pending remittance" queue. A forensic audit tracks these until the Credit Memo is actually issued.

• Is automation necessary?
  For vendors with >1,000 units per month, manual auditing is virtually impossible due to the sheer volume of remittance lines.

References

Amazon Ends Bulk Shortage Claims
https://www.threecolts.com/blog/amazon-ends-bulk-shortage-claims/

Amazon Vendor Alert: New 2 Year Shortage Claim Deadline
https://refundsmanager.com/amazon-vendor-alert-new-2-year-shortage-claim-deadline-could-cost-you-thousands-in-2025/

The Ultimate Guide to Amazon Shortage Claims 2025
https://www.barosintl.com/en/blog-en/the-ultimate-guide-to-amazon-shortage-claims-2025