eCommerce Seller GST Return Filing

Who is this service for

This page is for sellers on Amazon India, Flipkart, Meesho, Myntra, Nykaa, Ajio, Shopify, Etsy, and any other Indian marketplace. If you have a GSTIN and sell products online, you owe a monthly GST return cycle. The cycle is the same shape as a regular business. But the compliance layer is different. The marketplace deducts TCS under Section 52. It files GSTR-8 on your behalf. Your GSTR-1 must match what the marketplace reported. A mismatch is the fastest route to an ITC dispute and a departmental notice.

Surat textile sellers on Flipkart face peak-season compression. Flipkart Big Billion Days can generate a month's worth of sales in three days. GSTR-1 filed late or with incorrect HSN codes triggers a buyer's ITC rejection. For an Ahmedabad electronics reseller on Amazon, IGST-versus-CGST classification on interstate shipments is the live risk. For a Rajkot garment seller on Meesho, return-window adjustments and marketplace fee deductions change the net tax payable every month. These must reflect in GSTR-3B.

TCS Section 52 — what the marketplace deducts

Under Section 52 of the CGST Act, every e-commerce operator deducts Tax Collected at Source (TCS) at 1% of net taxable supplies. Amazon, Flipkart, Meesho, and Myntra all deduct this when they settle your account. The amount appears in your bank account as a net figure. The TCS is deposited with the government by the marketplace.

The marketplace then files GSTR-8 every month. GSTR-8 is a statement of all TCS it has collected and deposited on your behalf. This data auto-populates into your GSTR-2B as a locked figure. You cannot change it. You can only accept it or dispute it within the filing window.

Your GSTR-3B must show the TCS amount as a reduction of your gross tax liability. If your GSTR-1 declared higher outward supplies than what GSTR-8 shows, the portal flags a mismatch. ITC claims become disputed. The credit you thought you had is frozen until the dispute resolves. FinTax24 reconciles your marketplace settlement reports against GSTR-1 before filing. We catch mismatches before the GSTR-3B deadline, not after.

GSTR-8 and the monthly marketplace reconciliation

GSTR-8 is filed by the marketplace, not by you. It reports TCS collected on your sales. For Amazon sellers, the TCS statement is available in Seller Central under the Tax Document section. For Flipkart sellers, it appears in Seller Hub under Settlement Reports. Meesho suppliers find it in the Supplier Panel under TDS/TCS reports.

The monthly reconciliation process is: pull the GSTR-8 data from each marketplace, compare it against your sales records, identify discrepancies, and resolve before GSTR-3B filing. Common discrepancies include returns processed after the settlement period closed, fee adjustments, and promotional discounts that change the net taxable value.

Amazon seller GST workflow — step by step

Amazon India sellers follow this monthly cycle. Day 1-3: download the Tax Payment Report and TCS Statement from Seller Central. Day 4-7: reconcile net sales in the TCS statement against your sales register. Day 8-11: file GSTR-1 — B2C sales to individual buyers go in Table 5, B2B sales to business buyers with GSTIN go in Table 4. Day 12-20: prepare and file GSTR-3B — the TCS amount from GSTR-8 appears in Table 3.1 as a reduction of tax liability. Day 20-22: receive ARN and monthly summary.

Amazon also deducts TDS under Section 194Q when a seller's turnover exceeds ₹2,50,000 in a financial year. This is a separate deduction from TCS. It reduces the payment Amazon releases to your account. It does not appear in GSTR-8. It must be tracked separately in your books.

Flipkart seller GST workflow — step by step

Flipkart sellers follow the same GSTR-1 and GSTR-3B calendar. The key difference from Amazon is how Flipkart presents settlement data. The Flipkart Seller Hub settlement report shows net payable after platform fees, TCS, TDS, and return adjustments. The TCS component must be extracted separately for GSTR-3B reconciliation.

Flipkart deducts TCS at 1% on net taxable supplies. The Flipkart Seller Hub generates a monthly TCS certificate. Use this to verify what appears in GSTR-2B from the marketplace's GSTR-8 filing. If the GSTR-2B figure is lower than your TCS certificate, the marketplace may not have filed GSTR-8 correctly. Raise a ticket with Flipkart seller support before the GSTR-3B deadline.

Monthly vs quarterly vs composition scheme for eCommerce sellers

Most eCommerce sellers are regular taxpayers filing monthly. GSTR-1 is due by the 11th. GSTR-3B is due by the 20th. If your aggregate turnover is up to ₹5 crore, you can opt for the QRMP scheme. File GSTR-1 quarterly by the 13th of the month after the quarter ends. File GSTR-3B monthly by the 22nd-24th with payment only. QRMP reduces the filing frequency for GSTR-1 while keeping monthly tax payments intact.

Composition scheme sellers file CMP-08 quarterly instead of monthly GSTR-1 and GSTR-3B. The fee is a fixed percentage of turnover — 1% for manufacturers and traders, 5% for restaurants, 6% for service providers. Composition sellers cannot claim ITC. They cannot make inter-state sales. And critically — they cannot sell on eCommerce marketplaces. Section 52 of the CGST Act requires marketplaces to collect TCS only from registered sellers who are not composition dealers. If you are on the composition scheme, you cannot sell on Amazon, Flipkart, or Meesho. You must first migrate to the regular scheme.

Required documents each month

Each month you need: GST portal login credentials, Amazon Seller Central settlement report and TCS statement (or Flipkart/Meesho equivalent), sales invoices for any direct off-marketplace sales, purchase invoices for ITC claims, and bank statement for the filing period. FinTax24 uses the settlement report as the primary reconciliation source. We cross-check it against your sales data before preparing GSTR-1 and GSTR-3B.

FinTax24 eCommerce GST filing service

FinTax24 files GSTR-1 and GSTR-3B for eCommerce sellers across all 33 Gujarat districts. Our process reconciles marketplace settlement reports against GSTR-1 before filing. We flag TCS mismatches before the GSTR-3B deadline. We keep the GST portal and your books in sync. Single-store eCommerce sellers start at ₹1,699/month. Multi-store plans are available for sellers operating on two or more marketplaces under one GSTIN. The annual GSTR-9 reconciliation is included in yearly plans.

For the complete GST return filing calendar — including annual GSTR-9, composition scheme CMP-08, and the late fee and interest schedule — see our GST Return Filing Handbook 2026.

Save more with multi-month bundles. Visit the eCommerce GST Return Filing Bundle for bundled pricing.