An Amazon seller checks the bank statement and finds ₹4,20,000 credited, but the marketplace settlement report shows a different amount. Meanwhile, GST sales figures, TCS credits and TDS entries do not match the accounting records. With festive-season orders and returns adding to the workload, it becomes difficult to tell whether the difference is a delayed settlement, a tax-credit mismatch or an actual payment shortfall.
GST reconciliation for e-commerce sellers means matching marketplace sales, GST records, tax deductions, settlement reports and bank credits to identify discrepancies before filing returns. For Amazon and Flipkart sellers in India, the practical approach is to reconcile each platform separately, investigate unmatched transactions, verify GST TCS and income-tax TDS credits, and document every correction. Starting early gives you time to resolve genuine issues instead of relying on estimates during filing season.
Why Do Amazon and Flipkart Seller Records Show Different Figures?
Amazon and Flipkart settlement amounts rarely equal gross sales because several adjustments occur between an order and the final bank credit. GST, marketplace fees, refunds, shipping charges, reserves and settlement timing can all affect the amount received.
The first step is to distinguish a normal accounting difference from a genuine discrepancy. For example, an order placed on 30 September might be delivered in October, refunded later, or included in a settlement processed after the month closes.
Three common causes deserve attention:
- Settlement timing: Orders, deliveries, refunds and bank transfers may fall into different reporting periods.
- Marketplace deductions: Referral fees, fulfilment charges, shipping fees and other applicable charges reduce the payout.
- Tax reporting differences: GST TCS and income-tax TDS are reported through different systems and must be checked separately.
Do not classify every difference as a missing payout. That can lead to unnecessary claims or incorrect accounting entries.
What Is the Difference Between GST TCS and Income-Tax TDS?
GST TCS and income-tax TDS are different tax mechanisms. GST TCS relates to tax collected at source by an e-commerce operator under Section 52 of the CGST Act, while income-tax TDS concerns deductions under applicable income-tax provisions.
Confusing the two can make reconciliation harder because each has a separate reporting and verification process.
GST TCS
GST TCS is the amount collected by an eligible e-commerce operator on the net value of relevant taxable supplies under Section 52. Sellers should compare the marketplace’s tax-collected figures with the relevant GST portal records and investigate differences before finalising their returns.
The applicable rate and calculation should be verified against current GST rules. The CBIC’s GST sectoral FAQs explain the legal framework for e-commerce operators and TCS.
Income-tax TDS
Income-tax TDS is tax deducted under the applicable income-tax provisions. Sellers should check the relevant tax deduction details in Form 26AS and the Annual Information Statement (AIS), available through the Income Tax Department’s e-filing portal. The department explains these records in its official guidance on business and professional income.
A mismatch may result from incorrect PAN details, reporting delays or differences in the amount reported. Do not claim a credit solely because a marketplace report shows a deduction; verify the relevant tax record and applicable eligibility.
How to Perform Amazon Seller GST Reconciliation in 2026
Amazon seller GST reconciliation involves matching order-level sales and tax information with GST returns, settlement records and accounting entries. Start with the original transaction data instead of relying only on the net amount deposited into your bank account.
Step 1: Download the Amazon Seller Settlement Report
Log in to Amazon Seller Central and navigate to the payments or transaction reporting area. Download the available settlement reports and transaction details for the period under review.
Collect the following information wherever available:
- Order and transaction identifiers
- Gross sales and applicable GST
- Refunds and cancellations
- Marketplace fees and associated GST
- TCS deductions and settlement adjustments
- Settlement dates and bank transfer references
Keep the original files unchanged. Work on separate copies so you can trace every adjustment back to its source.
Step 2: Match Sales With GST Records
Compare the relevant Amazon sales transactions with your sales register and applicable GST return data. Check invoice values, taxable values, GST rates, place of supply and credit notes.
Returns need special attention. A refunded order does not automatically mean every related accounting or GST entry has been corrected. Verify the actual transaction, refund status and applicable credit-note treatment before adjusting the books.
Step 3: Reconcile TCS and Marketplace Fees
Compare Amazon’s TCS figures with the corresponding GST portal records. Separately check marketplace fees against invoices and expense entries.
A fee discrepancy is not necessarily a payout shortage. It may be a charge that was booked in the wrong period, an adjustment that has not been recorded, or an invoice that requires verification.
For a broader understanding of the relationship between selling charges and profitability, see HRL Infotechs’ Amazon seller profit calculation guide.
How Does Flipkart Seller Payment Reconciliation Work?
Flipkart seller payment reconciliation follows the same basic principle as Amazon reconciliation, but you must use Flipkart’s own settlement reports, fee records and transaction references. Never assume that both platforms use identical report structures or adjustment descriptions.
Step 1: Match Orders, Returns and Settlements
Download the available Flipkart payment and settlement reports from your seller account. Match order IDs, sales values, cancellations, refunds, fees, tax deductions and settlement references against your accounting records.
Pay particular attention to returned orders and transactions carried forward between settlement periods. A sale and its refund may appear in different reporting periods, so matching only monthly totals can hide the actual reason for a difference.
Step 2: Verify GST and TCS Entries
Compare Flipkart’s relevant sales and tax figures with your GST records. Investigate differences in taxable values, tax amounts, credit notes and TCS credits.
If the GST portal does not reflect an expected entry, first check the reporting period and source transaction. Then determine whether the issue requires a marketplace correction, a tax-record follow-up or an accounting adjustment.
How Can You Identify Missing Marketplace Payouts?
A missing payout is an amount that remains unexplained after valid deductions, refunds, timing differences and other adjustments have been accounted for. To identify one, reconcile each settlement against the underlying transactions and bank statement.
Consider this illustrative example:
| Reconciliation item | Amount |
|---|---|
| Eligible sales included in the settlement | ₹1,00,000 |
| Refunds and valid adjustments | ₹5,000 |
| Marketplace fees and related charges | ₹10,000 |
| Other applicable settlement deductions | ₹2,000 |
| Expected net settlement | ₹83,000 |
| Actual bank credit | ₹78,000 |
| Unexplained difference | ₹5,000 |
These figures are illustrative, not actual marketplace rates or a client result. The ₹5,000 difference is a discrepancy to investigate, not proof that the marketplace owes the seller that amount.
Check whether the difference relates to a partial transfer, reserve, subsequent adjustment, charge or another settlement reference. If the records still do not explain it, raise a support case with the relevant transaction IDs, settlement period, expected amount and bank credit evidence.
What Documents Should You Check Before Filing Season?
Keep a consistent set of records for each marketplace and financial period. This makes it easier to explain differences to your accountant, tax professional or marketplace support team.
Your reconciliation folder should contain:
- Amazon and Flipkart settlement reports.
- Order, sales, cancellation and refund reports.
- Marketplace fee invoices and credit notes.
- GST sales registers and relevant GST return records.
- GST portal records for TCS reconciliation.
- Form 26AS and AIS for income-tax TDS verification.
- Bank statements and marketplace support case references.
For sellers managing multiple marketplaces, a structured e-commerce account management workflow can help keep platform-level operational records organised alongside sales and settlement monitoring.
What Should You Do Before Filing Your Returns?
The safest approach is to investigate discrepancies in a fixed order rather than making last-minute accounting adjustments. Complete these checks before finalising the relevant returns and accounts.
- First, reconcile gross sales: Match orders, invoices, cancellations, returns and credit notes.
- Second, reconcile settlements: Compare expected net payouts with actual bank credits.
- Third, verify GST TCS: Check marketplace figures against the relevant GST portal records.
- Fourth, verify income-tax TDS: Review Form 26AS and AIS, and follow up on missing or incorrect entries.
- Fifth, resolve exceptions: Record the reason for every mismatch and retain supporting evidence.
- Finally, review before filing: Ask your accountant or tax professional to check unresolved differences and determine the appropriate treatment.
One practical trade-off is worth remembering: manual spreadsheets may be sufficient for a small seller with limited monthly transactions. However, as order volume, refunds and settlement adjustments grow, transaction-level matching becomes more reliable than comparing monthly totals alone.
Also, do not force every difference to zero by posting a balancing entry. A temporary timing difference, an unreported tax credit and a genuine short payment require different actions.
Need Help With Amazon and Flipkart Reconciliation?
If your marketplace sales, bank deposits and tax records are not matching, identify the source of the difference before filing season. HRL Infotechs provides e-commerce marketplace support and account management services that may help sellers organise platform operations and reporting workflows.
Explore the HRL Infotechs e-commerce services to discuss your marketplace requirements. For tax-credit eligibility, return adjustments and statutory filing decisions, work with a qualified tax professional.
Frequently Asked Questions
1. What is GST reconciliation for e-commerce sellers?
GST reconciliation for e-commerce sellers is the process of comparing marketplace sales, invoices, refunds, GST return figures and relevant tax records to identify differences. Amazon and Flipkart sellers should also review GST TCS records and retain supporting documents so that discrepancies can be investigated before filing the relevant returns.
2. How do I check Amazon seller TCS reconciliation?
Download the relevant Amazon settlement and tax transaction reports, then compare the reported TCS with the corresponding GST portal records. Check the transaction period, taxable supplies and applicable adjustments. If an expected entry is missing, verify whether the marketplace has reported it and follow up before making any unsupported credit claim.
3. How can I reconcile Flipkart seller payments with my bank statement?
Match each available Flipkart settlement reference with the corresponding bank credit. Account for refunds, marketplace fees, reserves and other documented adjustments. Investigate any remaining difference using transaction-level evidence, and raise a marketplace support request if the records cannot explain the amount.
4. What is the difference between GST TCS and income-tax TDS for Amazon sellers?
GST TCS is collected by an e-commerce operator under the GST framework, while income-tax TDS is deducted under applicable income-tax provisions. They are not interchangeable credits. Verify GST TCS through the relevant GST records and income-tax TDS through Form 26AS, AIS and other applicable documentation.
5. Why is my Amazon settlement amount lower than my sales?
The bank payout may be lower because marketplace fees, refunds, shipping charges, other adjustments or tax-related deductions reduce the amount transferred. Compare gross sales with the detailed settlement report before concluding that money is missing. Only an unexplained difference after valid adjustments should be treated as a potential payout issue.
6. When should sellers complete marketplace reconciliation?
Reconcile marketplace transactions regularly, ideally every month, rather than waiting until the filing deadline. Monthly checks help identify reporting delays, missing bank credits and incorrect tax entries while the supporting information is easier to retrieve. The appropriate filing dates and treatment depend on your business and the applicable tax requirements.
