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SPN consultants and Amazon sellers running hybrid Easy Ship plus FBA operations across 5–10 state-level GSTINs must file GSTR-1 per GSTIN mapping each invoice to the correct Table (4A, 5A, 7A, 7B) and place-of-supply, reconcile returns straddling two GSTR-1 periods, and track Section 52 TCS reversals across Amazon's revised GSTR-8 filings — all from the MTR template.
Ingest Amazon MTR monthly per GSTIN. Classify each invoice by B2B/B2C and intra-state vs inter-state for GSTR-1 table mapping. For Easy Ship, credit notes reverse output tax in the issue period (GSTR-1 Table 9B). For FBA, credit notes align to Amazon's return confirmation period — not the original sale period. Claim TCS Section 52 in GSTR-3B against GSTR-2B entries from Amazon's operator GSTIN and reverse any TCS that Amazon subsequently reverses via revised GSTR-8.
Amazon MTR connector, multi-GSTIN registry per FBA fulfilment state, place-of-supply logic per IGST Act Section 10, GSTR-1 table router (4A / 5A / 7A / 7B / 9B), return-period tracker for Easy Ship vs FBA, and TCS Section 52 reversal reconciliation against operator GSTR-8.
A filing-ready GSTR-1 per GSTIN with every invoice in the correct table, clean GSTR-3B output tax plus TCS Section 52 credit adjustment, return timing aligned to credit-note period rules, and an audit trail linking every MTR line to its GSTR-1 entry and GSTR-2B TCS credit.
An Amazon seller in the home and kitchen category runs a hybrid FBA plus Easy Ship operation across 8 FBA centres and their own warehouse in Mumbai. The SPN consultant files monthly GSTR-1 using Amazon’s MTR template. A single return initiated by a customer in Karnataka on an FBA order fulfilled from the Hyderabad FC touches three GSTINs, two GSTR-1 periods, and the Amazon Section 52 reversal stream. This article is for chartered accountants in Amazon’s SPN network and in-house finance teams managing GST reconciliation for Amazon India sellers.
What Amazon SPN GST Reconciliation Involves
Amazon SPN GST reconciliation is the monthly process of reconciling three data sets for an Amazon seller: the MTR (Merchant Tax Report) from Seller Central, the seller’s internal sales ledger or ERP, and the GSTR-2B TCS credits filed by Amazon. The output is a clean GSTR-1 ready for upload, a GSTR-3B with correct output tax and TCS credit adjustment, and an audit-ready trail linking each invoice, return, and TCS line to its source document.
The India-specific context is the multi-state FBA registration and the interaction between place-of-supply logic, return timing, and TCS reversal. A seller with FBA inventory in Haryana, Delhi, Maharashtra, Karnataka, Tamil Nadu, Telangana, West Bengal, and Gujarat holds 8 separate GSTINs — one per state. Each GSTIN files its own GSTR-1 and GSTR-3B monthly. An FBA order fulfilled from the Haryana FC to a Delhi customer is an inter-state supply filed under the Haryana GSTIN, not the seller’s principal place of business.
How Amazon SPN GST Reconciliation Works
Mapping the MTR to GSTR-1 Tables
The MTR is the primary input document. Each row represents an invoice — either a forward sale, a return credit note, or a tax adjustment. The reconciliation engine classifies each row into the correct GSTR-1 table: Table 4A for B2B intra-state and inter-state invoices, Table 5A for inter-state B2C invoices above ₹2.5 lakh, Table 7A for intra-state B2C aggregate by rate, Table 7B for inter-state B2C aggregate by state and rate, Table 9B for credit notes on prior-period invoices, and Table 9C for amendments. Misclassifying a row — for example, putting a Table 5A invoice into Table 7B — produces a GSTR-1 that fails validation or passes validation but creates GSTR-2A mismatches for the buyer.
Reconciling Easy Ship Returns to Credit Notes
Easy Ship returns are simpler than FBA returns because the inventory returns to the seller’s own warehouse and the seller controls the credit note timing. The reconciliation matches each return order ID in the Seller Central report to the original forward sale invoice, issues a GST credit note with reference to the original invoice, and reports the credit note in GSTR-1 Table 9B for the credit-note period. The output tax reversal hits GSTR-3B in the same period. If the original sale was in a prior GSTR-1 filing, the credit note amendment flow in Table 9B references the prior-period invoice number directly.
Reconciling FBA Returns and TCS Reversal Timing
FBA returns involve Amazon as the intermediary. The customer returns the item to Amazon’s return centre, Amazon inspects and either restocks, marks unsellable, or routes to the seller for disposal, and a settlement adjustment is raised against the seller’s payout. The seller must still issue a GST credit note to the buyer — the obligation to reverse output tax is on the seller, not Amazon. The Section 52 TCS reversal appears in a subsequent GSTR-8 filed by Amazon and flows into the seller’s GSTR-2B as a negative TCS entry. Reconciliation must match the original forward sale TCS to the reversal TCS across GSTR-2B periods — typically a one-to-two-month lag — to avoid double-counting TCS credit in GSTR-3B.
Amazon SPN GST Reconciliation Data Reference
| Data Source | Format | Primary Use | Reconciliation Target |
|---|---|---|---|
| MTR (Merchant Tax Report) | Monthly CSV from Seller Central | GSTR-1 invoice mapping | Seller ERP sales ledger |
| Business Reports | Order-level report | Revenue reconciliation | Settlement report, MTR |
| GSTR-2B JSON | Monthly from GST portal | TCS credit claim | Amazon Section 52 TCS line |
| Settlement Report | Bi-weekly from Seller Central | Bank payout reconciliation | Bank statement, MTR |
| FBA Inventory Report | Real-time from Seller Central | FC-state inventory tracking | Multi-state GSTR-1 splits |
India Compliance Angle: Multi-State FBA Registration and Section 10 Place-of-Supply
FBA inventory transfers between states are treated as stock transfers between two GSTINs of the same legal entity — a “branch transfer” under GST. Each transfer requires a tax invoice from the originating GSTIN to the destination GSTIN with applicable IGST, which is then claimed as ITC by the receiving FC-state GSTIN. These intra-company transfers appear in the seller’s GSTR-1 Table 4A (as B2B invoices to the other GSTIN) and in GSTR-2B of the receiving GSTIN. Forgetting to book these stock transfers produces inventory movements that are invisible in GST returns while physically real — a significant audit exposure in a GST scrutiny.
Place-of-supply for each FBA order is determined by Section 10 of the IGST Act based on the customer’s ship-to state compared with the state of the fulfilling FC. An FBA order picked from a Karnataka FC and shipped to a Tamil Nadu customer is an inter-state supply reported under the Karnataka GSTIN with 18% IGST — not under the seller’s principal place of business GSTIN. The MTR carries this correctly when downloaded per-GSTIN, but consolidating across GSTINs before filing requires careful sub-ledger separation.
Finance teams managing Amazon SPN filings alongside Flipkart reconciliation apply similar place-of-supply logic, though FBA’s multi-state registration requirement makes Amazon materially more complex. GST reconciliation software that supports multi-GSTIN filing workflows handles the FBA stock-transfer accounting natively. Payment gateway reconciliation pipelines reconcile the Amazon settlement payout against the MTR total to catch any timing gap between invoice-level GST reporting and cash-level settlement. The GST portal is the source of truth for GSTR-1 templates and the Section 52 TCS entries that Amazon files each month.
The following questions address the reconciliation issues Amazon SPN partners and sellers most frequently encounter.