How to File FBA Reconciliation Claims Correctly

For Amazon FBA sellers, unclaimed reimbursements from inventory discrepancies and fee errors can cost you thousands of dollars annually. With new policy changes as of March 10, 2025, Amazon now reimburses only manufacturing costs, excluding shipping and other expenses. Filing claims correctly and on time is more important than ever.

Key Takeaways:

• Sellers lose up to 3% of annual revenue due to FBA discrepancies.

• Claims must now focus on manufacturing costs, not total expenses.

• Deadlines are strict: e.g., 15–75 days for removal orders, 60 days for damaged inventory.

• Accurate documentation (invoices, photos, reports) is critical for success.

• Automated tools like Refunzo simplify tracking and filing claims, recovering thousands of dollars in missed refunds.

Steps to File Claims:

1. Identify discrepancies: Use Amazon's inventory reports to spot issues.

2. Gather documentation: Include invoices, proof of delivery, and photos.

3. File claims in Seller Central: Provide all required details and evidence.

4. Track claims: Monitor case status and follow up if needed.

Proper preparation, regular audits, and automation can help recover up to 5% of your FBA costs. Don’t leave money on the table - stay compliant, meet deadlines, and use tools to streamline the process.

Amazon's FBA Reconciliation Policies Explained

What FBA Reconciliation Claims Are

Amazon's FBA reconciliation claims give sellers a way to recover costs when inventory is lost, damaged, or mishandled within Amazon's fulfillment network. These claims address situations like items disappearing from fulfillment centers, damage during storage or handling, or discrepancies in inventory counts. They also cover instances of incorrect charges, such as storage or fulfillment fees applied by mistake.

Claims can include issues like shipment discrepancies, inventory destruction, transfer delays, or fee errors. The goal is to reimburse sellers for the manufacturing cost of affected items.

Understanding the types of claims is just the first step. Sellers must also familiarize themselves with Amazon’s specific policies to ensure their claims are eligible and submitted correctly.

Policy Requirements for Filing Claims

Starting March 10, 2025, Amazon will calculate reimbursements based solely on manufacturing costs. This excludes shipping, handling, customs duties, storage, and other related expenses. However, there’s an exception: if an item is lost or damaged after a customer places an order, Amazon will reimburse the sales price from the original order, minus applicable fees.

Sellers have two ways to establish manufacturing costs. You can either input the actual costs on the "Manage Your Sourcing Cost" page or through the IDR portal in Seller Central. If no cost is provided, Amazon will estimate the value using market comparisons, similar product prices, or wholesale benchmarks.

Deadlines for filing claims are stricter in 2025. For removal orders involving lost-in-transit items, claims must be filed within 15–75 days of the shipment creation date or within 60 days after a return is delivered. If a claim is denied, sellers have 30 days to appeal. Missing these deadlines results in automatic denial, with no chance of recovery.

"Without sufficient documentation, reimbursement claims may be reduced or denied." – Emplicit

Proper documentation is essential. Required materials include SKU details, unit costs, dates, and timestamped evidence such as invoices, packing slips, delivery confirmations, photos of damage, inventory reports, Bills of Lading, and proof-of-value. Any gaps or inconsistencies in these documents can lead to claim rejections.

To qualify for claims, sellers must meet specific requirements: active FBA registration, compliant shipment records, matching quantities, non-canceled shipments, and a well-maintained account in good standing.

Account health plays a major role in eligibility. Amazon uses automated systems and manual reviews to monitor compliance, and your Account Health Rating (AHR) reflects how well you adhere to their policies. Serious violations can harm both your ability to file claims and your overall account standing.

"Compliance is not a one-time task – Amazon updates its policies regularly, and staying informed is critical for maintaining account health and customer trust." – Emplicit

Sticking to these policies isn’t just about getting reimbursements - it’s about protecting your business. Non-compliance can lead to reduced payouts, account suspensions, restricted listings, loss of Featured Offer status, withheld funds, and even negative customer feedback. These consequences can disrupt operations and hurt your cash flow, making it critical to stay on top of policy updates and requirements.

How to File Claims on Seller Central for Different Amazon FBA Discrepancies - Reimbursements Guide

How to Prepare Before Filing a Reconciliation Claim

When it comes to filing a reconciliation claim with Amazon, preparation is everything. Amazon's strict documentation requirements mean that having the right materials and a well-organized system can be the deciding factor between a successful reimbursement and a denied claim.

Required Documentation to Gather

To get started, you’ll need to gather specific documentation for every claim, no matter the type of discrepancy.

• Core documents: These include invoices, receipts, order confirmations, and proof of inventory ownership. For shipments, make sure to include packing slips and proof of delivery.

• Removal order claims: If your claim involves a removal order, you’ll need the removal order ID, shipment ID, exact quantity of affected units, and a detailed explanation of the issue. This could mean describing missing components, damages, incorrect items, or undelivered shipments. For issues like wrong products, Amazon often asks for images showing differences in material, serial numbers, or model numbers.

• Photographic evidence: For damaged inventory, clear, timestamped photos are essential. These should highlight the damage and include key product identifiers to help Amazon’s team quickly understand the problem without needing further clarification.

"Common documentation required includes invoices, packing slips, proof of delivery, photographic evidence of damage or loss, and inventory reconciliation reports. The specific data and documentation required may vary depending on the type of reimbursement claim you're submitting." - GETIDA

• Bills of lading: For LTL (Less Than Truckload) and FTL (Full Truckload) shipments, bills of lading are non-negotiable. These documents should detail the number of boxes and total shipment weight, giving Amazon the necessary shipping details to investigate.

How to Audit Your Inventory Properly

Once your documentation is ready, the next step is to audit your inventory. Regular audits are key to identifying discrepancies early, and systematic approaches work better than manual spot-checking.

Automated reconciliation tools can be a game-changer. These tools connect directly to your Amazon Seller Central account and analyze your inventory for discrepancies. They check for issues like mismatched shipment stock counts, damaged returns, or lost inventory using over 20 criteria. The result? A detailed report that outlines potential reimbursements Amazon may owe you, complete with SKU-level details and estimated dollar amounts.

"I am very appreciative of this team. They have done a great job finding money which was owed to me by Amazon due to lost and damaged inventory." - Rob C.

While automation simplifies the process, manual verification remains important. Cross-check your records with Amazon’s reports, paying attention to sudden unit drops or unexplained fees. If you notice recurring discrepancies for the same SKU, it might point to a larger issue at a specific fulfillment center.

How to Organize Records for Compliance

Once you’ve identified discrepancies, keeping your records organized is crucial. Well-maintained records not only improve your chances of successful claims but also help protect your account’s health.

• Set up a filing system: Organize invoices by date and supplier, group shipment records by fulfillment center, and create separate folders for each type of claim. Use consistent naming conventions that include dates in MM/DD/YYYY format and dollar amounts in standard US currency format ($X,XXX.XX).

• Archive settlement reports: These reports from Seller Central provide transaction-level details essential for supporting claims. Store them in chronological order and reconcile each report with your bank deposits to catch discrepancies early.

• Categorize financial records: Create distinct categories for income from different Amazon marketplaces and expenses like referral fees, FBA fees, storage fees, advertising costs, and removal fees. Keep inventory-related expenses separate and track returns, refunds, and reimbursements clearly.

• Establish monthly and quarterly procedures: Regularly reconcile bank accounts, credit cards, and Amazon settlements. Review accounts payable, allocate prepaid expenses, and calculate fixed asset depreciation. Lock accounting periods after closing to safeguard your documentation trail.

"When submitting a case, include all relevant documentation and screenshots to help Amazon understand the issue clearly. This will reduce the need for back-and-forth correspondence and speed up resolution time." - Marketplace Valet

Finally, document your standard procedures for bookkeeping and reconciliation. Write clear instructions for processes like settlement report processing, month-end closing, tax filing, and inventory reconciliation. This ensures consistency, simplifies training for team members, and helps accountants understand your system.

Disorganized records can lead to delays, disputes, and even denied claims. When Amazon requests additional information, being able to provide it quickly and accurately makes all the difference. Plus, well-kept records go beyond FBA claims - they support tax compliance, audits, and smarter business decisions.

Step-by-Step Guide to Filing an FBA Reconciliation Claim

Once you’ve organized your records and conducted a thorough audit, you’re ready to start the process of filing a reconciliation claim. Below, we’ll walk you through each step to ensure you can handle this process smoothly and effectively.

How to Find and Investigate Discrepancies

The first step is pinpointing where your inventory records don’t align with Amazon’s data. These mismatches, or inventory discrepancies, occur when there’s a difference between the inventory levels Amazon reports and what you actually have. Catching these issues early can save you time and money.

To begin, head to Seller Central and review Amazon’s inventory reports. Navigate to the Reports tab, select Fulfillment, and locate key reports like Inventory Adjustments and FBA Customer Returns. These reports are your go-to tools for uncovering discrepancies. For example:

• Inventory Adjustments: Details changes Amazon made to your inventory.

• FBA Customer Returns: Shows items that were returned and should be back in sellable condition.

Common causes of discrepancies include human error, damaged goods, improper labeling, short shipments, or errors at Amazon’s fulfillment centers. Occasionally, you might also encounter theft, loss, or software glitches.

Here’s what to look for:

• Sudden drops in inventory levels that don’t match your sales.

• Items marked as “unfulfillable” without a clear reason.

• Shipment quantities that don’t align with your records.

Pay extra attention to high-value SKUs. These items often represent the largest reimbursement opportunities. Cross-check your shipment records against Amazon’s received quantities, and if you notice recurring problems with specific SKUs or fulfillment centers, document these patterns. Once you’ve identified the discrepancies, you’re ready to file your claim.

How to File a Claim Through Seller Central

With your discrepancies identified and documentation in hand, you can file your claim through Seller Central. There are two main options for submitting claims: the Help section or the Inventory Defect & Reimbursement (IDR) portal.

1. Using the Help Section:

   • Go to the Help section in Seller Central.

   • Select Get Support, then navigate to Selling on Amazon > Your Account > Other Account Issues.

2. Using the IDR Portal:

   • Navigate to Reports, select Fulfillment, click Show More, and choose Inventory Adjustments. This allows you to dispute specific inventory changes made by Amazon.

When filing your claim, include all the necessary details:

• Transaction ID

• Reimbursement amount

• A clear explanation of the discrepancy

Attach all relevant documents, such as invoices, packing slips, photos of damaged items, or bills of lading for shipments. Be specific in your description. For instance, instead of saying, “My inventory is wrong,” provide detailed information like:
"Shipment FBA15XXXXX was delivered on 10/15/2024 with 50 units of ASIN B08XXXXX, but only 45 units were checked into inventory. Attached are the packing slip and bill of lading confirming delivery."

Amazon’s support team typically responds within 24–48 hours, though complex cases may take longer. If they request additional information, respond quickly to avoid delays or case closures.

How to Track Claims and Timelines

Once your claim is submitted, staying on top of it is crucial. While Amazon usually processes reimbursements within 45 days, consistent monitoring ensures nothing gets overlooked.

To track your claim:

• Go to the Help section where you filed the claim. Each case is assigned a unique case ID for easy reference.

• Amazon will update the case with their findings, requests for more information, or final decisions.

To check reimbursement status:

• Open your Seller Central Dashboard.

• Click the Reports tab, select Payments, and review the Transaction View. Approved reimbursements will appear as credits in your account, usually within 1–2 business days after resolution.

"Regular monitoring and analysis of these reimbursement reports are crucial for effective amazon reimbursement tracking. It helps ensure that you are adequately compensated for returns and can provide valuable insights into your business operations." – KwickMetrics

Set a weekly routine to review inventory adjustments, settlement reports, and active cases. This proactive approach ensures you catch issues early and keep your claims moving forward. If a case remains unresolved for more than a week, follow up using the original case ID.

For better organization, create a simple spreadsheet to track your claims. Include columns for:

• Case ID

• Submission date

• Claim amount

• Status

• Follow-up dates

"Efficient reimbursement tracking involves a combination of proactive monitoring, leveraging automation tools, maintaining accurate records, staying informed about policies, conducting internal audits, and fostering communication with Amazon Support." – KwickMetrics

Perform internal audits at least once a month to cross-check your records with Amazon’s data. Regular reconciliation helps you spot new discrepancies early, laying the groundwork for future claims. The faster you identify and report issues, the better your chances of receiving a reimbursement.

How to Avoid Common Mistakes and Stay Compliant

Once you've mastered the filing process, the next step is steering clear of common errors that could derail your efforts. Filing FBA reconciliation claims might seem straightforward, but many sellers make mistakes that lead to rejected claims or missed reimbursements. Knowing Amazon's compliance rules and avoiding these pitfalls can be the difference between recovering thousands of dollars or losing it entirely. Sellers often face significant losses due to unnoticed overcharges or poor record-keeping.

Key Policy Compliance Rules

Even with a solid filing process, sticking to Amazon's compliance rules is essential to protect your reimbursements. Amazon has strict criteria for accepting reconciliation claims. The most important requirement? Your item must be registered in FBA and meet all inventory and product guidelines. Additionally, the quantities you ship must match your shipping plan exactly - any mismatch can immediately disqualify your claim.

Your seller account must also be active and in good standing when filing. Items pending disposal or damaged by customers are not eligible for reimbursement. Amazon enforces strict timeframes for filing claims, which vary depending on the claim type:

• Fulfillment center operations claims (lost or damaged items): Must be filed within 60 days of the item being reported lost or damaged.

• FBA customer returns claims: Filing is allowed between 60–120 days after the customer refund or replacement date. Filing before the 60-day mark is not permitted.

• Removal claims for lost-in-transit items: Must be filed within 15–75 days of the shipment creation date. For all other removal claims, the window is 60 days from the shipment delivery date.

"Many reimbursements, including FBA inbound inventory discrepancies and overcharged fees, are not automatically reimbursed by Amazon as the responsibility is on the seller to reconcile and notify Amazon once discovered."
– GETIDA

Starting March 10, 2025, Amazon will limit reimbursements to manufacturing costs only - excluding shipping, handling, and customs fees. This makes maintaining accurate cost documentation even more critical for successful claims.

Common Mistakes and How to Prevent Them

One of the biggest mistakes sellers make is missing Amazon's strict eligibility windows. With some claims requiring submission within as little as 60 days, many sellers realize discrepancies too late. This can result in losing up to 40% of potential reimbursements.

Another frequent issue is incomplete or inaccurate documentation. Missing or incorrect supporting documents are a common reason claims are rejected. Amazon requires specific proof for each claim type, and even one missing piece can lead to an automatic denial.

Filing too early is another common error, especially for customer return claims. Sellers often don’t realize they must wait at least 60 days after a customer refund before submitting these claims. Filing prematurely will automatically disqualify the claim.

Choosing the wrong claim category is another stumbling block. Misclassifying your claim can cause delays and force you to restart the process.

Finally, poor record-keeping can sabotage even valid claims. Without organized invoices, purchase orders, and shipment records, sellers may struggle to provide the required timestamped proof. It's estimated that up to 20% of inventory is misclassified, which can lead to unnecessary overcharges.

To avoid these issues, keep your documentation well-organized and accessible. Wait 30–45 days for Amazon to correct errors before filing claims. This practice, recommended by top sellers, helps prevent premature filings and ensures you capture all eligible discrepancies. Consistently maintaining organized records strengthens your compliance and increases the likelihood of successful claims.

Using Automation for Better Accuracy

Manual reconciliation is not only time-consuming but also prone to human error. Automated tools, on the other hand, are far more reliable, with a 90% claim success rate compared to manual methods.

Automated tools can identify discrepancies that manual processes often miss. They provide end-to-end tracking, logging every step of inventory movement from departure to receipt. This eliminates "in-transit" blind spots and offers a clearer view of your stock. These tools also ensure compliance by automatically compiling shipment and inventory data, submitting claims within Amazon’s eligibility windows, and maintaining a detailed record history with user logs and timestamps.

For example, in September 2025, Refunzo helped a kitchen tools brand recover $15,600 in FBA reimbursements within 30 days. The brand had been unaware of missing and damaged inventory claims. Using advanced tracking technology, Refunzo reconciled accounts against over 21 criteria, uncovering unpaid claims for lost inventory, damaged stock, and incorrect reimbursements.

"Monthly closure and reports used to take us 2-3 days to gain an understanding of our FBA. I now have strong confidence; it's a no-brainer to provide accurate inventory numbers to Finance for the monthly closure."
– François Piccin, COO

Refunzo offers a free lifetime reconciliation service for Amazon FBA, with over 20 criteria checks. They provide detailed reports on potential reimbursements, allowing you to claim refunds yourself or let Refunzo handle the process for a capped commission fee. This automation ensures you never miss eligibility windows while maintaining the precision needed for successful claims.

"Sellers should never lose money because of system errors they cannot control. Refunzo ensures every claim is filed, tracked, and recovered. It allows sellers to focus on building their business, while we handle the reimbursement side."
– Jimi Patel, Amazon business expert and director of eStore Factory

How Refunzo Simplifies Reconciliation

Keeping accurate records and conducting manual audits are essential, but they can only take you so far. That’s where automation steps in, and Refunzo makes the reconciliation process seamless with its fully automated system. By connecting directly to your Amazon Seller Central account, Refunzo identifies discrepancies across FBA categories like shipments, fees, and inventory - no manual tracking required. This not only minimizes errors but also ensures every eligible reimbursement is accounted for, offering a smarter way to handle FBA reconciliation.

Refunzo's Main Features

Refunzo provides a lifetime free reconciliation service that performs detailed checks using over 21 criteria. It automatically flags discrepancies in areas such as shipments, payments, inventory, fees, and refunds. Specific issues, like stock deducted after shipment closure, damaged shipments, or returns, are also identified.

The platform simplifies the process by generating real-time refund estimates with clear breakdowns. Instead of wrestling with Amazon’s complex reports, you get organized insights into potential reimbursements by category and issue type. This level of clarity helps you decide which claims to pursue.

Refunzo’s reputation is solid, with a 5 out of 5 stars rating on the Amazon Selling Partner Appstore, showcasing its effectiveness and dependability. It addresses common FBA challenges, from inventory discrepancies to fee overcharges, which can add up to significant recoveries over time.

"Our system makes the process effortless, whether sellers want to submit the claims themselves or let our team handle it on their behalf." - Jimi Patel, Amazon business expert and director of eStore Factory

Benefits of Automated Reconciliation

Automated reconciliation saves you from the tedious manual work that often results in missed reimbursements. It ensures you don’t overlook eligible claims due to time constraints or errors, helping you stay compliant with Amazon’s tight eligibility windows and policies.

By directly connecting to Amazon Seller Central, Refunzo eliminates the need to manually download and cross-check multiple reports. Its real-time monitoring catches discrepancies as they happen, giving you ample time to file claims within Amazon’s strict deadlines.

Users frequently report recovering thousands to tens of thousands of dollars in reimbursements they would have otherwise missed. The system excels at identifying complex issues, like fee miscalculations and inventory errors, that are often overlooked during manual reviews.

"Been using them for a while - efficient service, reasonable price and seem to constantly be finding money that Amazon owes me." - Danny

"Refunzo is great. Have found me 10's of thousands of dollars. Professional and efficient." - Doug Joyce

Optional Claim Filing Service

For sellers who prefer a hands-off approach, Refunzo offers a claim filing service that takes care of the entire reimbursement process. For 15% of the reimbursed amount, capped at $5,000, the service handles everything - from opening support cases with Amazon to providing evidence and following up until refunds are deposited into your account.

Each claim is meticulously reviewed to ensure accuracy, and Refunzo’s team provides expert support to meet Amazon’s documentation and policy requirements. You’ll only need to authenticate a credit card during setup, and no charges are applied unless reimbursements are successfully credited to your account.

This service not only saves time by automating discrepancy detection but also manages the complex tasks of claim submission and tracking. This allows sellers to focus on growing their business, knowing that no eligible reimbursement will slip through the cracks.

"I mainly use Refunzo for finding inventory that was lost or damaged at Amazon's warehouse and they are worth every penny of the commission they charge. I will continue using them for a long time." - Robert Cuttler

"Sellers should never lose money because of system errors they cannot control. Refunzo ensures every claim is filed, tracked, and recovered. It allows sellers to focus on building their business, while we handle the reimbursement side." - Jimi Patel, Amazon business expert and director of eStore Factory

Conclusion: Get More Reimbursements with Accurate Claims

In this guide, we’ve covered the essential steps for accurate FBA reconciliation. Filing claims properly isn’t just about following procedures - it’s about recovering money that’s rightfully yours and safeguarding your profits. Let’s recap the key strategies that make this possible.

Success in maximizing reimbursements boils down to three main areas: diligent preparation, adherence to Amazon’s policies, and leveraging automation to catch discrepancies that might slip through manual reviews.

Preparation is key. Keeping detailed records and conducting regular inventory audits can significantly increase the amount you recover. With Amazon’s 2025 policy update shifting reimbursement calculations to sourcing costs rather than sale prices, precise documentation has become even more critical for ensuring you claim the maximum value.

Routine audits and reconciliation deliver measurable results. Sellers who stay consistent with these practices often recover up to 30% more funds compared to those relying solely on manual or infrequent reviews. Many sellers report recovering thousands - or even tens of thousands - of dollars that would have otherwise been lost.

Once your preparation is solid, automation takes your reconciliation process to the next level. Automation is a game-changer. Amazon’s intricate fee structures and tight claim deadlines make manual reconciliation both time-consuming and error-prone. Tools like Refunzo simplify the process by running thorough checks across over 20 criteria, spotting issues in real time, and ensuring you meet every deadline.

The advantages of automation are clear. Unlike manual processes, which are labor-intensive and prone to mistakes, automated tools deliver higher recovery rates with less effort. Platforms like Refunzo ensure accuracy and help you capture every eligible reimbursement.

FAQs

What documents do I need to file an FBA reconciliation claim with Amazon?

To submit an Amazon FBA reconciliation claim, you’ll need to collect certain documents to back up your case. These usually include:

• Proof of inventory ownership

• Proof of delivery

• Shipping manifests

• Delivery confirmations

• Inventory logs

• Photos of damaged items

• Product dimension and weight details

Making sure your documentation is thorough and accurate can help the process go more smoothly and improve your chances of getting reimbursed for any lost or damaged inventory.

How can Refunzo help simplify and improve the process of filing Amazon FBA reconciliation claims?

Refunzo takes the hassle out of filing Amazon FBA reconciliation claims by automating the detection of discrepancies with over 20 specific checks. This means less manual work, fewer mistakes, and a more precise way to uncover potential reimbursements.

The platform generates detailed reports that help sellers pinpoint issues quickly. From there, they can either file claims on their own or let Refunzo take care of it. This not only saves time but also accelerates reimbursements, offering sellers confidence that everything is managed smoothly.

What should I do if my FBA reconciliation claim is denied or needs more information?

If your FBA reconciliation claim gets denied or Amazon asks for more details, the first step is to check the shipment details in your Seller Central account under the 'Contents' tab. Pay close attention to any inconsistencies, like mismatched unit counts or missing paperwork.

If Amazon requests additional documents, make sure to upload the relevant files through the shipment reconciliation process. Follow their instructions carefully to avoid unnecessary delays. While resolution times can vary, they usually take between 2 and 30 days. You can track the progress of your claim in the Shipping Queue section of Seller Central.

Staying on top of requests and keeping your documentation organized can help move things along more smoothly and get your claim resolved faster.

Related Blog Posts

• 5 Ways to Maximize Your Amazon FBA Reimbursement Claims

• Understanding Amazon's FBA Reimbursement Policy

• Amazon FBA Inventory Adjustments: Key Reports

• How to Spot Shipment Discrepancies in FBA