What to Do When Amazon Misplaces Your FBA Inventory

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Sep 7, 2025
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min
What to Do When Amazon Misplaces Your FBA Inventory

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It's one of the most frustrating experiences for an FBA seller: you meticulously pack and ship 100 units to Amazon, but the final report says they only received 98. Or you check your inventory dashboard and notice that a handful of units have simply vanished. In the controlled chaos of Amazon's massive fulfillment network, inventory discrepancies happen.

The good news is that Amazon has a policy to reimburse sellers for inventory that is lost or damaged when it is under their control. The challenge is that this process is rarely automatic. The responsibility is on you, the seller, to identify these discrepancies, file a precise claim with the correct documentation, and follow up. This guide provides a clear process for reconciling your inventory and recovering your money.

1. Where Do Discrepancies Happen?

Inventory loss typically occurs in two main scenarios:

  1. Inbound Shipment Discrepancies: This happens when the quantity of units Amazon checks in at the fulfillment center does not match the quantity you declared in your shipping plan.
  2. Warehouse Discrepancies: This happens after your inventory has been successfully received. A unit can be lost or damaged while being moved within a warehouse, during transfer to another fulfillment center, or before being packed for a customer order.

2. How to Reconcile Inbound Shipments (Step-by-Step)

This is the most common type of claim you will file.

  • Step 1: Be Patient. This is crucial. Your shipment may be split and sent to multiple fulfillment centers. It can take several days, or even weeks during peak season (like Q4), for the full shipment to be checked in. In your "Manage FBA Shipments" queue, each shipment has a "Reconcile" tab. This tab will show you the exact date on which you become eligible to open an investigation. Do not open a case before this date.
  • Step 2: Gather Your Proof. To get reimbursed, you need to prove what you sent. Amazon will require two key documents:
    • Proof of Ownership: An invoice from your supplier or manufacturer, dated before your shipment, that clearly shows the purchase of the missing products.
    • Proof of Delivery: Proof that the shipment was delivered to and signed for by Amazon. For small parcel shipments, this is the carrier tracking confirmation. For larger pallet (LTL/FTL) shipments, this is the signed Bill of Lading (BOL).
  • Step 3: File the Claim. Once the reconciliation date arrives, go to the "Reconcile" tab. You will see a dropdown menu next to the missing items. Select "Missing - Please Research," enter the number of missing units, and upload your proof documents.
  • Step 4: Follow Up. Monitor the case you created in your Case Log. Respond promptly and professionally to any requests for more information from the Seller Support team.

3. How to Find Warehouse Discrepancies

Finding items that go missing after they've been received is more complex, as it won't be flagged in your shipping queue.

  • The Key Tool: The Inventory Ledger Report. This is the most powerful inventory report in Seller Central (found under Reports > Fulfillment). It is a detailed, transaction-by-transaction log of every unit's movement, from receiving to sale to return.
  • How to Audit: Regularly download this report and filter the "Reason" column for codes like "Damaged at Amazon Fulfillment Center" or "Lost in Warehouse." Amazon should automatically reimburse you for these discrepancies within 30 days. However, sometimes these are missed.
  • Filing a Manual Claim: If you identify a lost or damaged unit in the report for which you were not reimbursed after 30-45 days, you can open a manual case with Seller Support. In your case, provide a screenshot of the relevant line from the Inventory Ledger report and state the ASIN, date, and transaction ID of the discrepancy you are claiming.

4. How Reimbursements Work

If your claim is approved, Amazon will reimburse you for the lost product.

  • Reimbursement Value: Amazon calculates the value based on the item's average selling price over the past 90 days, from which they subtract the standard Referral Fee and FBA fees. Essentially, you receive the net profit you would have made from a successful sale.
  • Cash or Replacement: Amazon reserves the right to either issue a cash reimbursement to your account or replace the lost item with an identical unit from their own inventory.

Auditing FBA inventory reports and managing reimbursement cases is a time-consuming but vital task that directly impacts your bottom line. As a full-service agency, Sitruna's account management team handles this entire reconciliation process for our clients, ensuring that no lost unit goes unreimbursed.

Useful Resources

Conclusion: Protect Your Assets

Think of reconciling your FBA inventory as a critical financial task, just like bookkeeping. It is your responsibility to hold Amazon accountable for the valuable inventory you entrust to their care. By implementing a regular audit process, you can recover thousands in otherwise lost revenue and protect your profit margins.

Need an expert team to manage your day-to-day Amazon operations, including inventory reconciliation? Schedule a free discovery call with the Sitruna team at www.sitruna.com/meet to learn how our operational expertise can protect your profits.

Our Amazon team is ready to help you succeed.

Book a discovery call with us today!

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