GST registration for online sellers on Amazon and Flipkart

Why GST Registration Is Compulsory for Amazon and Flipkart Sellers

Under Section 24 of the CGST Act, any person supplying goods through an e-commerce operator is required to obtain GST registration compulsorily, irrespective of the usual turnover limit of ₹40 lakh (goods) or ₹20 lakh (services) that applies to offline businesses. This means:

• A first-time seller with zero prior sales still needs a GSTIN to open an Amazon Seller Central or Flipkart Seller Hub account.
• The threshold exemption available to small offline traders does not apply to online sellers of goods.
• Sellers of certain notified services (subject to specific conditions) may have limited relief, but goods sellers almost always need registration upfront.
• Marketplaces validate your GSTIN through the GSTN system during onboarding, so an incorrect or inactive number will block your listing approval.

This is one of the most common reasons new sellers get stuck at the marketplace onboarding stage, and it's why getting GST registration done correctly, on the first attempt, matters so much.

Documents Required for GST Registration for E-commerce Sellers

The document list is largely the same as any regular GST registration, with a few additions relevant to online selling:

If you are just starting out and don't have a registered business yet, you can still apply as a sole proprietorship, or set up a Private Limited Company if you want a more structured entity for scaling on multiple marketplaces.

Step-by-Step GST Registration Process for Amazon & Flipkart Sellers

Here is the exact sequence setupfiling.in follows for online seller clients, from document collection to a live GSTIN ready for marketplace onboarding:

1. Free eligibility & document check: Our GST experts review your PAN, address proof, and business structure to confirm the correct registration category.
2. Application drafting on the GST portal: We prepare and submit Form GST REG-01 with accurate business details and the correct HSN/SAC codes for your product category.
3. Aadhaar authentication: You complete a quick Aadhaar-based e-KYC, which speeds up approval significantly.
4. ARN generation: An Application Reference Number is generated instantly, confirming your application is in process.
5. Query resolution (if any): If the GST officer raises a clarification, our team responds on your behalf within the timeline.
6. GSTIN issued: Once approved, you receive your 15-digit GSTIN and registration certificate.
7. Marketplace linking: You enter the GSTIN in Amazon Seller Central or Flipkart Seller Hub to complete your seller profile and start listing products.

Most applications are approved within 3-7 working days when documents are in order, though Aadhaar-authenticated applications are often faster than manual verification.

TCS Under GST: What Every Amazon and Flipkart Seller Must Understand

Amazon and Flipkart are classified as e-commerce operators and are required to deduct Tax Collected at Source (TCS) at 1% (0.5% CGST + 0.5% SGST, or 1% IGST for interstate sales) on the net taxable value of goods sold through their platform, before making payouts to sellers. This deducted amount reflects in your GSTR-2B/electronic cash ledger and can be claimed as credit while filing your GST returns.

Sellers frequently lose out on this credit simply because they don't reconcile TCS entries against actual sales, which directly affects working capital. Regular GST return filing ensures this TCS credit is claimed correctly every month.

GST Compliance After Registration: What Online Sellers Must Keep Filing

Getting the GSTIN is only step one. Marketplace sellers have ongoing monthly and quarterly obligations:

• GSTR-1: Outward supply details, typically filed monthly or quarterly under the QRMP scheme.
• GSTR-3B: Summary return with tax Payment, filed monthly — see our detailed guide on GSTR-3B filing.
• TCS reconciliation: Matching Amazon/Flipkart TCS statements with your GSTR-2B to claim correct credit.
• GST amendment: If you add a new warehouse, business line, or bank account, an amendment to your GST registration is required.
• LUT filing: Relevant if you also export goods internationally through marketplaces — see LUT in GST.
• Composition scheme evaluation: Note that sellers supplying goods through e-commerce operators are generally not eligible for the GST composition scheme, so regular scheme compliance applies.

Missing returns even for a few months can lead to GSTIN suspension, which immediately blocks your marketplace listings — this is why many sellers prefer ongoing professional support rather than handling filings themselves.

Common Mistakes Online Sellers Make During GST Registration

• Wrong principal place of business: Using a home address without proper NOC/rent agreement, causing rejection.
• Incorrect HSN code selection: Leads to tax rate mismatches later during return filing.
• Ignoring additional place of business: Required if you use a third-party warehouse or Amazon/Flipkart fulfilment centre in another state.
• Not registering in multiple states: If you store inventory in an Amazon FBA warehouse located in a different state, a separate GST registration in that state may be required.
• Delayed Aadhaar authentication: Skipping this step slows down approval significantly.

Why Sellers Choose SetupFiling.in for GST Registration

SetupFiling.in is an online business services platform founded by Chartered Accountants, Company Secretaries, and Trademark Attorneys with 15+ years of combined expertise. We have assisted 50,000+ entrepreneurs, startups, and established businesses across India with GST registration, GST return filing, trademark filing, FSSAI licensing, and other compliance needs.

• End-to-end GST registration handled by qualified professionals, not automated forms.
• Dedicated support for Amazon FBA and Flipkart multi-state warehouse registrations.
• Ongoing GST return filing and TCS reconciliation support after registration.
• Transparent pricing with no hidden charges.
• Direct WhatsApp support for quick queries and document submission.

Frequently Asked Questions