Manual vs Automated FBA Reconciliation: Which to Choose?

Struggling with Amazon FBA reconciliation? Here's the quick answer: manual reconciliation gives you control but is time-consuming, while automated tools are faster and recover more reimbursements.

Key Points:

• Manual Reconciliation: Best for small sellers with fewer orders. Requires time and effort but has no software costs.

• Automated Tools: Ideal for scaling businesses. Saves time, reduces errors, and increases reimbursement recovery by up to 166%.

Quick Comparison:

Bottom Line: Small sellers can manage manually, but automation is a must for medium to large businesses to save time and maximize profits.

Review of EVERY Amazon Reimbursement Software - The Best Way to Request Reimbursement

FBA Reconciliation Basics

FBA reconciliation means comparing your sales and inventory data with Amazon's system of fees, payments, and transaction reports. With the 2025 reimbursement rule changes, understanding these processes is more important than ever to keep your operations profitable.

Main Reconciliation Problems

Amazon sellers face several challenges when reconciling their FBA accounts. The most common issues involve inventory discrepancies, fee errors, and the updated reimbursement rules introduced in March 2025:

These stricter deadlines and changes to reimbursement calculations mean sellers need to monitor their accounts more closely. Common problems include missing inventory from inbound shipments, incorrect FBA fees due to size or weight issues, and errors in processing customer returns. Tackling these issues requires a clear plan for reconciliation.

Reconciliation Objectives

To address these challenges, sellers must set clear goals. The main purpose of FBA reconciliation is to ensure accurate financial records and claim all eligible reimbursements.

Key objectives include:

• Inventory Accuracy: Review Inventory Adjustments reports daily to identify any discrepancies.

• Fee Verification: Regularly check FBA fees using the Fee Preview tool to catch errors.

• Reimbursement Recovery: File claims for lost or damaged items within the new 60-day window.

To meet these goals, sellers should maintain precise production cost records, organize digital claim documentation, and monitor their accounts consistently. The Fee Preview tool is especially helpful for spotting size and weight errors before they affect your bottom line.

Experts suggest scheduling reconciliation reviews every 45 days for the best results.

Manual Reconciliation Methods

Handling FBA reconciliation manually involves a clear process to address mismatches between your shipped inventory and Amazon's records. With Amazon's policy limiting claim windows to 60 days, staying organized and precise is more important than ever. This process also helps you understand when switching to automation might be worth considering.

Step-by-Step Manual Process

Here's how the manual reconciliation process works in Amazon Seller Central:

1. Access Shipping Records: Log in to Seller Central and go to Inventory > Manage FBA Shipments.

2. Review Discrepancies: Look for issues in the "Units located" messages and the "Status" column.

3. Analyze Records: Match the quantities you shipped with the units Amazon received.

4. Submit Research Requests: For missing units, select "Missing – Please Research", and for extra units, choose "Unexpected – Please Research".

5. Provide Evidence: Submit details like shipping box information, product codes, and proof of purchase, especially for claims nearing the 60-day deadline.

"Reconciling your Amazon shipments is a very important and very simple accounting work step to include in your monthly routine. If an item you've shipped is lost by Amazon, you may be entitled to a reimbursement." - Anna Hill, CPA

Manual Method Pros

There are some clear benefits to using a manual approach:

Manual Method Cons

However, manual reconciliation has its challenges:

Staying on top of your records is crucial to meet Amazon's 60-day claim window. Next, let’s look at how automation can streamline these tasks and save you time.

Automated Reconciliation Tools

Manual reconciliation can be tedious and time-consuming. Automated tools, on the other hand, streamline the process by using advanced algorithms to detect issues and compile claim evidence, saving sellers both time and effort.

How Automation Works

Automated reconciliation tools keep a constant eye on your Amazon seller account. They analyze data like sales, payments, inventory, shipments, fees, and refunds. By cross-checking these data points, the software identifies reimbursement opportunities and gathers the necessary evidence to file claims - solving many of the challenges associated with manual reconciliation.

Benefits of Automation

Automated reconciliation offers several key advantages over manual methods:

Popular Reconciliation Tools

Here’s a quick overview of some of the top FBA reconciliation tools:

One success story comes from Bases Loaded, a baseball equipment retailer. They switched from manual reconciliation to an automated system using Webgility integrated with QuickBooks. This shift allowed them to process 1,000 orders automatically, doubling their revenue and growing order volume 21 times in just a few months.

These tools also prioritize security, using encryption to safeguard financial data while simplifying the reconciliation process. Choosing the right tool depends on the size of your business and your specific needs.

Manual vs Automated: Direct Comparison

Comparison Chart

Here's a side-by-side look at how manual and automated reconciliation stack up:

This chart highlights the strengths and weaknesses of each approach, making it easier to identify what suits your needs.

Best Method for Your Size

The right method depends on how many orders your business processes each month:

• Small Sellers (Under 1,000 monthly orders):
  

  Manual reconciliation can work if you have the time to dedicate. It's a cost-effective option for straightforward operations. For a bit of automation, tools like Refunzo's free service are worth exploring.

• Medium-Sized Sellers (1,000–5,000 monthly orders):
  

  A combined approach - manual checks paired with basic automation - works well here. As your transaction volume grows, automation becomes more valuable and delivers a better return on investment.

• Large Sellers (5,000+ monthly orders):
  

  Full automation is a must. Manual processes at this scale are inefficient and offer little return on investment. Comprehensive automation tools ensure scalability and efficiency.

Revenue loss is a critical consideration. For Amazon sellers, unclaimed reimbursements can account for 1–3% of annual revenue. Investing in automation often pays off quickly by recovering more claims and cutting operational costs.

How to Pick Your Method

After comparing manual and automated approaches, decide which one fits your business needs best.

Business Requirements Check

Use the following questions to assess your business needs and determine the right reconciliation method:

When Manual Works Best

Manual reconciliation is a good choice for businesses with smaller order volumes, fewer SKUs, and operations limited to one marketplace. It’s ideal if you prefer full control over the process and have team members available to handle data entry and monitoring. For sellers in this category, manual reconciliation can be both manageable and cost-effective, requiring about 10 hours of work per week. However, if your operations don’t align with these factors, automation may be a better fit.

When to Use Software

As your business grows, automation becomes more practical. Automated tools are particularly useful if:

• Your order volume increases significantly

• You’re expanding to new marketplaces or experiencing rapid growth

• Managing a larger number of SKUs makes inventory tracking harder

• Manual reconciliation takes more than 10 hours a week

• You need real-time monitoring and quick adjustments

"For those considering transitioning from manual to automated repricing, Repricer provides a 14-day free trial. This allows you to evaluate whether it not only saves time and effort but also enhances your sales and profit potential."
– Ronan White, SEO and content marketing executive at Repricer

You can also try free tools like Refunzo’s lifetime free reconciliation service, which includes 21-point checks and detailed reports. This is a low-risk way to explore automation without upfront costs.

For businesses scaling up, automation minimizes errors, reduces inventory losses, and keeps you competitive. U.S. retailers, for example, face an average inventory shrinkage rate of 1.38%, amounting to nearly $50 billion in losses annually. Automation can help by:

• Cutting down on human errors during data entry

• Providing real-time monitoring

• Boosting Buy Box win rates

• Offering better insights into competitors

• Supporting growth with scalable solutions

Conclusion

The way you handle FBA reconciliation has a direct impact on your finances and workflow. Studies show that automated solutions can cut reconciliation time by up to 95%, and users report recovering up to 166% more with tools like Getida.

For businesses relying on manual processes, reconciling 100 accounts can take over 800 hours a month and cost more than $6,500 in labor. This sharp comparison highlights the importance of selecting a method that matches your business size and needs.

Small-scale operations might manage with manual methods, but as your business grows, automation becomes essential for better accuracy and efficiency. Tools like Refunzo make the shift easier with their lifetime free reconciliation service, offering a simple way to move from manual to automated processes.

Related posts

• 7 Common FBA Reimbursement Issues Every Seller Should Know

• Amazon FBA Reconciliation Checklist for 2025

• Understanding Amazon's FBA Reimbursement Policy

• Common Recordkeeping Mistakes in FBA Audits