How to Reconcile Payments From Amazon and Flipkart: A Step-by-Step Guide for Sellers

Reconcile Payments From Amazon and Flipkart

Every rupee matters when you’re running an e-commerce business, yet countless sellers on Amazon and Flipkart unknowingly leave money on the table simply because their payments go unverified.

After fees deduction, returns, and adjustments, what lands in your bank account often looks quite different from what you actually earned. That’s where e-commerce payment reconciliation can close that gap.

In this blog, we’ll walk you through how to reconcile payments on Amazon and Flipkart, every report you need to pull, every step in the process, every common mistake sellers make, and how to make sure not a single rupee goes unaccounted for. Let’s get started!

What Happens If Marketplace Payment Reconciliation Is Missed or Delayed?

Ignoring reconciliation across marketplaces like Amazon or Flipkart can lead to financial losses and operational blind spots. Over time, small discrepancies can accumulate into significant revenue leakage.

Some common consequences include:

1. Unnoticed Inventory Losses

Inventory may get lost or misplaced during fulfillment, warehouse transfers, or returns processing. If reconciliation is not done regularly, these missing units may never be identified.

• Example: 50 units of a product priced at ₹3,000 go missing during transfer = ₹1,50,000 loss
• Multiple such incidents throughout the year can significantly impact margins

Without proper tracking, sellers may not realize the inventory discrepancy

2. Missed Reimbursements

Marketplaces often compensate sellers for lost or damaged items, but claims usually have strict timelines. If reconciliation is delayed, sellers may miss the window to request reimbursement.

Typical claim windows may include:

• Lost inventory claims within a defined time frame
• Damaged product reimbursements
• Incorrect deductions or fee adjustments
• Customer returns that were never added back to inventory

Missing these timelines means the eligible amount may never be recovered.

Different Claim Windows for Amazon and Flipkart

Different Claim Windows for Amazon and Flipkart

3. Incorrect Fee Deductions

Marketplace settlement systems can sometimes apply incorrect fees or charges. Without reconciliation, these errors may go unnoticed.

Common examples include:

• Higher-than-expected commission charges
• Incorrect shipping or logistics fees
• Duplicate fulfillment charges
• Miscalculated storage or service fees

Even a small overcharge of ₹50–₹100 per order can add up to thousands of rupees over hundreds of orders.

4. Return and Refund Mismatches

Returned orders may not always follow the expected flow. Sellers might encounter cases where:

• Returned products are not added back to inventory
• Refunds are processed without proper adjustments
• Reverse logistics costs are higher than expected

Without reconciliation, these discrepancies can affect both inventory accuracy and financial records.

5. Accounting and Compliance Issues

If marketplace settlements do not match the actual amounts received in bank deposits, maintaining accurate financial records becomes difficult. This can create complications during:

• GST reporting
• Financial audits
• Internal accounting reviews

Regular e-commerce reconciliation ensures that order revenue, marketplace deductions, and bank payouts align correctly, reducing financial and compliance risks.

Now that you know what’s at stake, the first step to fixing it is making sure you have the right data and documents in place before you begin reconciliation.

Data and Documents Required for Amazon Payment Reconciliation

To reconcile payouts from Amazon, sellers need a set of reports available in Amazon Seller Central. These reports help match order activity, deductions, and final payouts.

1. All Orders Report

A complete record of orders, including order ID, product details, order value, and status.

2. Merchant Transaction Reports (MTR — B2B & B2C)

Provides transaction-level details such as invoice data, taxes, and order values.

3. Disbursement Report

Shows the payments released by Amazon to the seller for a specific settlement cycle.

4. All Returns Report

Contains details of returned orders and related refund transactions.

5. FBA Returns Report

Lists returns for orders fulfilled through Amazon’s fulfillment network.

6. Order-Level Reimbursement Report

Tracks reimbursements issued for lost, damaged, or incorrectly handled orders.

7. SKU Master File

A product reference list containing all SKUs used to map orders with items.

8. Bank Statement

Used to verify that the settlement amount credited by Amazon matches the payout received in the bank account.

Data and Reports Required for Flipkart Payment Reconciliation

To reconcile payouts from Flipkart, sellers must review several reports available in Flipkart Seller Hub. These reports help track orders, deductions, returns, and final settlements.

1. Order Report

Contains details of all orders placed on Flipkart, including order ID, item information, quantity, and order status. It forms the base dataset for matching sales with settlement records.

2. Sales Report

Provides a summary of sales transactions, including fulfilled orders, cancelled orders, returns, and the total invoice value collected from customers. It may also include information related to cashback or promotional adjustments.

3. Settlement Report

Shows the payout breakdown for each order. It includes deductions such as commission, fixed fees, shipping charges, collection fees, and applicable taxes like TDS or TCS, along with the final settlement amount credited to the seller.

4. Ads and Non-Order Charges

Certain settlement files may also contain sheets for advertising costs or other service-related deductions, such as warehousing or platform service fees.

5. Returns Report

Includes data on returned or RTO orders processed by Flipkart. Sellers use this report to verify refunds, reverse logistics charges, and inventory movement related to returns.

Key Challenges in Amazon and Flipkart Payment Reconciliation

Reconciling payments on marketplaces like Amazon and Flipkart can be challenging due to multiple reports, deductions, and settlement cycles.

1. Delayed Settlements

Payments may sometimes be credited later than the expected settlement cycle, affecting cash flow.

2. Mismatch in Settlement Amounts

The payout received may differ from the expected amount due to discounts, taxes, or pricing adjustments.

3. Complex Fee Structures

Marketplaces apply multiple fees such as commission, shipping, and return logistics charges, which can be difficult to track.

4. High Transaction Volumes

Handling and reconciling thousands of orders across reports can be time-consuming.

5. Data Discrepancies

Differences between internal order records and marketplace reports may require careful verification.

6. Returns and Adjustment Tracking

Returns, refunds, and reverse logistics charges may appear in different settlement cycles.

7. Manual Reconciliation Processes

Without automation, reconciliation involves manual data checks, increasing effort and the risk of errors.

General Steps for Manual Marketplace Reconciliation

When sellers reconcile payments manually for marketplaces like Amazon and Flipkart, the process typically involves downloading and verifying multiple reports from the seller dashboards.

Typical manual reconciliation steps include:

1. Download Marketplace Reports

Sellers usually download 5–8 Excel reports, such as order reports, settlement reports, sales reports, return reports, and transaction reports.

2. Match Settlements With Bank Deposits

Settlement amounts from the marketplace are compared with the payouts received in the bank account.

3. Break Down Transaction Details

Each order is analyzed to verify revenue, commissions, shipping fees, taxes, discounts, and other deductions.

4. Verify Inventory Movements

Returned items, cancellations, and fulfilled orders are checked against internal inventory records.

5. Identify Discrepancies And Raise Claims

Any missing payments, incorrect deductions, or reimbursement issues must be identified and reported.

6. Update Accounting Records

Settlement data is then mapped to revenue, expenses, and taxes in the accounting system.

Why Manual Reconciliation Becomes Difficult

In practice, this process can quickly become confusing and time-consuming, especially when sellers operate across multiple marketplaces. Teams often end up juggling between multiple spreadsheets to track orders, settlements, fees, and returns.

Common challenges include:

• Managing multiple Excel reports from different marketplaces
• Switching between several spreadsheets to match orders with settlements
• Difficulty tracking returns, refunds, and adjustments across cycles
• Verifying different fee structures for each platform
• Increased chances of manual errors in calculations
• Spending significant time on data validation instead of business operations

Because of these complexities, manual reconciliation often becomes exhausting and inefficient as order volumes grow.

How Unicommerce Can Help with Amazon and Flipkart Payment Reconciliation

Chasing settlement discrepancies manually is one of the biggest hidden profit drains for Amazon & Flipkart sellers.

Let’s say you ship 500 orders in a month, only to find that 40 returns were never credited back, 15 orders show payment gaps in your settlement report, and 3 SPF claim windows have already closed before you even noticed.

As order volumes scale, these numbers only grow, and spreadsheets simply can’t keep up. That’s where UniReco by Unicommerce comes in.

UniReco is an automated payment reconciliation and returns management solution built for e-commerce sellers. It matches orders, payments, and returns across marketplaces in real time, so discrepancies get caught early, not after the claim window has closed.

Here’s what UniReco does for your business:

• Automated Reconciliation — Fetches sales, payment, and return files from Amazon, Flipkart, and other marketplaces automatically, no manual report downloads needed.
• Real-Time Payment Visibility — Track pending payments, overdue settlements, and leakages across all channels from one dashboard.
• Discrepancy and Overcharge Detection — Flags missed payments, overcharged commissions, and incorrect fees before you lose the window to dispute them.
• Returns Reconciliation — Tracks delivered, returned, and pending items with full transparency, including reverse logistics costs.
• SPF Claim Alerts — Identifies eligible orders and sends deadline alerts so no reimbursement opportunity is missed.
• Order-Wise Revenue Visibility — Transaction-level breakdown of charges and expected revenue to help you contest deductions and track true profitability.
• GST-Ready Reports — Compliance-ready financial reports for accurate, audit-friendly tax reporting.
• Scalable Across Channels — Works across two marketplaces or twenty, maintaining accuracy as your business grows.

So, stop guessing with marketplace reconciliation. Catch every payment discrepancy with UniReco today!

This blog was originally published on the Unicommerce blog page, where we regularly share in-depth insights on e-commerce operations, inventory control, fulfilment, and growth challenges. You can explore more related topics, industry analysis, and practical guidance by visiting Unicommerce.