Amazon India GST Reconciliation Handbook:
MTR, GSTR-1, TCS & Audit Defence

MTR stands for Merchant Tax Report — Amazon India's monthly export of every sale's GST breakdown (CGST, SGST, IGST), TCS deduction, and net taxable amount, per order. Download from Seller Central → Reports → Tax Document Library → Merchant Tax Report (B2B and B2C have separate reports). Download monthly. Each row has the buyer's state, GSTIN if B2B, place of supply, GST rate, and amounts. Match these against your GSTR-1 filing every month.

Same total GST rate, different split based on buyer's location relative to seller. Intra-state sale (seller and buyer in same state, e.g., Karnataka → Karnataka): split 50-50 into CGST + SGST (e.g., 18% becomes 9% CGST + 9% SGST). Inter-state sale (different states, e.g., Karnataka → Tamil Nadu): the full GST goes as IGST (18% IGST). Special case: union territories use UTGST instead of SGST. Amazon's MTR report tells you which type each sale is.

They are two separate deductions from your payout. GST TCS is collected under Section 52 of the CGST Act; once you accept it on the GST portal, it is credited to your electronic cash ledger. Income-tax TDS is deducted under Section 194-O of the Income Tax Act; it appears in Form 26AS and is claimed when you file your income-tax return. Rates are set by law for the transaction period, so use the exact amount shown on your settlement and confirm the treatment with your CA.

GSTR-1 is your outward supply return — every sale invoice (or invoice consolidated for B2C) filed monthly. GSTR-3B is your summary self-assessment + payment return — total sales, total ITC claimed, net GST paid. The reconciliation: total taxable value in GSTR-1 should match total taxable supplies in GSTR-3B for the same month. Mismatches trigger GSTN system flags and notices. For Amazon sellers, the MTR report is the source of truth — both filings should match the MTR's monthly totals.

When a customer returns an order and is refunded: the original sale's GST is reversed via a credit note in your GSTR-1 (filed in the month the return happens, not the original sale month). The output GST liability for that month is reduced. If you've already paid the GST in the original month, you can claim the reduction in your next month's GSTR-3B. Most CAs handle this automatically but it's a common audit-flag area — ensure your MTR refund rows are reflected as credit notes.

Often, yes. If Amazon stores your inventory in fulfilment centres in other states, those locations generally need to be registered as additional places of business, which can mean a separate GST registration in each such state. Requirements depend on your setup, so confirm with your CA before sending inventory to a new state.

GST audits typically start with a notice asking for 5 documents: GSTR-1 + GSTR-3B for the year, MTR exports for the year, your Inventory Register, your purchase invoices (for ITC claimed), and bank statements. The auditor reconciles your filed returns against Amazon's reported sales (Amazon files its own consolidated TCS report under your GSTIN). Common red flags: GSTR-1 < MTR (under-reported sales), ITC claimed without invoice, missing return credit notes. Prepare an audit-defence pack monthly, not yearly — Seller Wolf can auto-export this.