Marketplace Settlement Reconciliation: Amazon, Flipkart, Meesho

Your Amazon order says ₹1,180. Your bank says ₹938. Somewhere between the two, ₹242 went missing, and the settlement report lists six lines you've never looked at closely.

Most of that ₹242 isn't lost. Only about ₹200 is a real cost. The rest is tax credit sitting in three different government ledgers, and it stays yours only if you claim it. Settlement reconciliation is how you find it, and how you catch the deductions that really are mistakes.

Where the money goes: one order, line by line

Take a single order on any of the big three marketplaces. The fees below are illustrative (your category's rate card will differ), but the tax treatment is the same everywhere.

Line	Amount	What it is	Where you get it back
Sale price (incl. 18% GST)	₹1,180	₹1,000 taxable + ₹180 output GST	— (you owe the ₹180 in GSTR-3B)
Commission (10% of ₹1,180)	− ₹118	Marketplace fee	Business expense
Closing / fixed fee	− ₹20	Marketplace fee	Business expense
Shipping / logistics	− ₹62	Marketplace fee	Business expense
GST on fees (18% of ₹200)	− ₹36	Tax on the marketplace's service to you	ITC, via the fee invoice in GSTR-2B
GST TCS (0.5% of ₹1,000)	− ₹5	Tax collected under Section 52	GST cash ledger, via "TDS and TCS Credit Received"
Income-tax TDS (0.1% of ₹1,000)	− ₹1	Section 194-O TDS	Your ITR, via Form 26AS / AIS
Payout	₹938

On Meesho the fee lines look different (no commission, but a logistics fee and a platform fee instead). They still carry 18% GST, and the rest of the table works the same way.

Two details matter here. TCS has been 0.5% since 10 July 2024 (it was 1% before, and plenty of guides still say 1%). And the 194-O TDS is calculated on the amount excluding GST when GST is shown separately, per CBDT Circular 17/2020, so it's ₹1, not ₹1.18.

Of the ₹242 gap, ₹200 is cost. The other ₹42 is yours to claim. At ₹10 lakh a month in sales that's roughly ₹42,000 a month, which is real working capital if you never accept the TCS credit or miss fee invoices in GSTR-2B.

Want to run this for your own price and category? The Marketplace Profit Calculator does the same split, and the GST calculator splits a GST-inclusive price into taxable value and tax.

The three-way match, every month

Reconciliation isn't one check. It's three, and each one catches a different kind of error.

1. Sales report ↔ GSTR-1

Total the taxable value and GST from your marketplace orders (or sales/tax) report for the calendar month, net of returns. That total should equal what you declared in GSTR-1.

The usual break: returns. The marketplace processes a return, but no credit note goes into your GSTR-1, so you've paid GST on a sale that didn't happen. If you sell on more than one marketplace, do this per platform before adding them up.

2. Settlement report ↔ bank statement

Each settlement in the payments report should match one credit in your bank account, to the rupee. Settlements follow the platform's cycle, not the calendar: a sale on 28 October may be paid in November. Reconcile by settlement ID, not by month.

The usual break: a settlement that's short because of a reserve or holdback (money held against expected returns), or a negative balance from last cycle being recovered.

3. Deductions ↔ government records

This is the one most sellers skip, and it's where the money is. Split every deduction in the settlement report into four buckets and check each against its own record.

Bucket	Check it against	If it doesn't match
Fees	Fee invoices + your rate card	Raise a ticket for wrong weight slab or category fee
GST on fees	GSTR-2B (fee invoices must be issued to your GSTIN)	Ask the marketplace to correct the GSTIN on the invoice
GST TCS	GSTR-8, shown on the portal's TDS and TCS Credit Received tab	Accept it monthly. Unaccepted TCS never reaches your cash ledger
Income-tax TDS	Form 26AS / AIS	Ask the marketplace to correct its TDS return before you file ITR

Our GSTR-2A vs GSTR-2B guide explains why 2B is the one to reconcile against, and GST on marketplace fees covers who can claim the fee GST and the 1 November 2026 refund change. For TCS, the TCS refund guide walks through accepting the credit and what to do with an excess balance. For TDS, see Section 194O explained.

The five leaks that show up every month

Once the three checks are done, whatever is left over almost always falls into one of these:

1. Returns with no credit note. You keep paying output GST on goods that came back. Fix it in the next GSTR-1.
2. Unpaid reimbursement claims. A return arrives damaged or never arrives, and the claim you filed with the marketplace is still open. Track claim IDs in a sheet; they expire.
3. Wrong fee slab. Shipping charged on a higher weight than the item, or commission at a different category's rate. One wrong slab repeated across 500 orders adds up fast.
4. TCS you never accepted. The marketplace reported it in GSTR-8, but you didn't accept it on the portal, so it's sitting outside your cash ledger.
5. Fee invoices outside GSTR-2B. Usually a seller account mapped to the wrong state's GSTIN, which happens a lot with multi-warehouse sellers.

Leaks 1, 4 and 5 are tax credits you've already paid for. Leaks 2 and 3 are cash the marketplace owes you.

Why this matters more in November and December

Two deadlines make this the month to clean up FY 2025-26:

• 30 November 2026 is the last date to claim ITC on FY 2025-26 invoices, including marketplace fee invoices you missed (or your GSTR-9 filing date, if earlier). See our ITC claim deadline guide.
• 31 December 2026 is the GSTR-9 deadline. Your annual return pulls together GSTR-1, GSTR-3B, GSTR-2B and GSTR-8. If the monthly reconciliations above are done, GSTR-9 is mostly addition. If they aren't, it's archaeology. Sellers above ₹5 crore also have the GSTR-9C TCS and Section 9(5) reconciliation to do.

What to do now

1. Pick last month and do the three-way match once, by hand, in a spreadsheet. One month is enough to see where your gaps are.
2. Accept pending TCS credit on the GST portal (Services → Returns → TDS and TCS Credit Received).
3. Check GSTR-2B for every marketplace's fee invoices for FY 2025-26 before 30 November.
4. List open reimbursement claims and follow up on anything older than a month.
5. If you sell above a few hundred orders a month, a spreadsheet stops scaling. Our GST software comparison covers tools that import settlement reports directly.

Platform-specific walkthroughs: Amazon seller GST guide · Flipkart seller GST guide · Meesho GST calculator.

Would rather a CA did the monthly reconciliation? Share your details and a CA partner in our referral network will contact you with a quote. Dhanaay doesn't file or reconcile anything itself, and sharing your details is free.

Sources: TCS rate, Notification 15/2024-Central Tax (0.5% from 10 July 2024); TCS credit flow, GST portal TDS and TCS Credit Received; 194-O base excludes GST shown separately, CBDT Circular 17/2020. Read 31 October 2026. Fee amounts in the example are illustrative, not any platform's current rate card.