Selling on Amazon, Flipkart and other marketplaces brings reach and volume, but the money that reaches your bank account rarely matches the sales figure on your dashboard. Commissions, shipping charges, storage fees, GST on fees, tax collected at source, TDS, returns, promotions and reserves all sit in between. Regular e-commerce settlement reconciliation is the only way to know your real margin, claim every credit you are entitled to and keep your GST and income-tax filings consistent.
This guide explains what goes into a marketplace settlement, a step-by-step reconciliation method, a worked example for a single order, and the common leakages sellers recover once they start reconciling properly.
Key takeaways
- Reconcile at the order level: each order ID should trace from the order report to the settlement report and then to the bank credit.
- Marketplace fees carry 18% GST, which is usually available as input tax credit when the invoices are correctly captured.
- GST TCS at 0.5% of net taxable supplies and income-tax TDS at 0.1% under section 194-O are deducted from payouts and must be claimed back through returns.
- Returns, customer refunds, RTO shipments and reimbursement claims are where most money is lost if not tracked.
- A monthly routine tied to your GST filing calendar keeps the books, returns and marketplace data aligned.
What a marketplace settlement contains
Marketplaces pay sellers periodically, often weekly or more frequently, net of deductions. A typical settlement includes:
- Order value: the selling price including GST, and shipping charges collected from customers where applicable.
- Marketplace fees: referral or commission fee, fixed or closing fee, shipping or weight handling fee, pick-and-pack and storage fees for fulfilment programmes, and payment collection fees.
- GST on fees: charged at 18% by the marketplace on its services.
- GST TCS: collected by the marketplace under section 52 of the CGST Act.
- Income-tax TDS: deducted under section 194-O (carried forward under the Income-tax Act, 2025).
- Adjustments: customer returns, refunds, cancellations, promotional discounts, advertising charges and reserves or holds.
- Reimbursements: compensation for lost or damaged inventory and other claims.
Each marketplace provides downloadable order, payment and tax reports. Save them monthly, because older reports can be harder to retrieve later.
A worked example for one order
A seller sells a product at ₹1,180 including GST at 18% (taxable value ₹1,000, GST ₹180). The settlement for this order shows:
| Item | Amount (₹) |
|---|---|
| Order value received from customer | 1,180 |
| Less: commission, closing and shipping fees | (200) |
| Less: GST on fees at 18% | (36) |
| Less: GST TCS at 0.5% of taxable value | (5) |
| Less: TDS under section 194-O at 0.1% | (1) |
| Net amount credited to bank | 938 |
In the books, this should be recorded as:
- Sales ₹1,000 and output GST ₹180 (reported in GSTR-1 and GSTR-3B)
- Marketplace fees ₹200 as an expense, with ₹36 input tax credit
- TCS ₹5 as a receivable, claimed from the electronic cash ledger after it appears in your TCS credit data
- TDS ₹1 as advance tax credit, claimed in the income-tax return
- Bank ₹938
Most sellers make the mistake of booking ₹938 as sales. That understates turnover, loses the ITC on fees and leaves TCS and TDS unclaimed. Our article on GST for e-commerce sellers explains the TCS mechanism in more detail.
Step-by-step e-commerce settlement reconciliation
- Download monthly reports: order or sales report, settlement or payment report, tax invoice reports for fees, returns report and inventory reports for fulfilment stock.
- Build an order-level sheet: list every order ID with invoice value, GST, fees, TCS, TDS, adjustments and net settlement.
- Match to the bank: group orders by settlement ID and match each payout to the bank credit. Our guide on bank reconciliation best practices covers the bank side.
- Verify fees: compare charged fees with the marketplace’s published rate card for the category and weight slab. Flag unusual charges.
- Track returns and cancellations: ensure refunded orders are reversed in sales through credit notes, and that returned stock is received back in saleable condition or claimed.
- Reconcile GST TCS: match TCS in your records with the TCS data filed by the marketplace, and accept it on the GST portal so the credit reaches the cash ledger.
- Reconcile TDS: match 194-O TDS with the tax credit statement before filing the income-tax return.
- Book summary entries: post monthly journal entries from the reconciled sheet and keep the working as support.
Common leakages and how to recover them
- Weight or dimension disputes: incorrect weight slabs lead to higher shipping fees; raise a correction with the marketplace.
- Lost or damaged inventory in fulfilment centres: file reimbursement claims within the marketplace’s time window.
- Customer returns not received: a refund issued but no product returned can often be claimed under seller protection programmes.
- Duplicate or incorrect fee charges: especially after policy changes or promotions.
- Unclaimed TCS and TDS: small per order but significant across a year.
- Reserves not released: check that held amounts are released after the holding period.
Sellers who start reconciling regularly often find that recoveries alone cover the cost of the effort. Keep a simple claims log with the order ID, issue, date raised, amount and outcome, so nothing slips past the marketplace’s claim window.
Aligning with GST and income-tax filings
- Sales in GSTR-1 should match your order-level data, and the marketplace’s TCS statement should agree with your sales net of returns.
- ITC on marketplace fees should reconcile with the invoices appearing in your GSTR-2B.
- Turnover in the income-tax return should match GST turnover and the marketplace data reflected in the Annual Information Statement.
- Stock in fulfilment centres should be included in closing inventory at the year end.
Frequently asked questions
How often should Amazon and Flipkart settlements be reconciled?
At least monthly, before filing GST returns. High-volume sellers often reconcile weekly with each settlement cycle.
Can I claim ITC on marketplace commission?
Yes, GST charged on marketplace fees is generally available as input tax credit if you are a registered seller and the invoices appear in your GSTR-2B.
How is GST TCS deducted by marketplaces recovered?
It is credited to your electronic cash ledger after you accept it on the GST portal, and can then be used to pay tax or claimed as a refund.
Should I record sales at the net settlement amount?
No. Record sales at the full invoice value and account for fees, TCS and TDS separately, so that turnover, credits and expenses are all correct.
If you sell on marketplaces and would like help setting up a monthly settlement reconciliation, our e-commerce accounting team would be happy to help.
This article is general information based on the law as of September 2026, and is not legal or tax advice. Please check the facts of your own case with a professional before acting.


