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E-Commerce GST & Accounting Amazon, Flipkart & D2C

Specialised GST compliance, TCS reconciliation, accounting, and income tax filing for e-commerce sellers on Amazon, Flipkart, Meesho, and D2C brands. We handle the platform-specific complexities that general accountants miss.

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What We Cover

Our Services

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GST Registration for E-Commerce Sellers
Mandatory GST registration for all marketplace sellers (Amazon, Flipkart, Meesho) regardless of turnover, and for D2C brands crossing the applicable threshold. Multi-state registration for sellers with warehouses in multiple states.
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Monthly GSTR-1 & GSTR-3B Filing
Accurate GSTR-1 filing reconciled with your sales reports from each marketplace. GSTR-3B with ITC claims on advertising, packaging, courier, warehousing, and platform fees.
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TCS Reconciliation — Section 394
E-commerce operators (Amazon, Flipkart) deduct TCS at 1% on net sales. We reconcile TCS deducted across all platforms with Form 26AS and claim it correctly in GST returns — a common source of errors for marketplace sellers.
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GSTR-9 Annual Return & GSTR-9C
Annual GST return reconciling your full year's turnover, ITC, and tax payments. GSTR-9C audit report for sellers with turnover above Rs.5 crore.
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E-Commerce Accounting & Bookkeeping
Monthly accounting reconciled with Amazon/Flipkart settlement statements, courier charges, platform fees, returns, and refunds. Accurate P&L by SKU category. COGS and inventory tracking.
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ITR Filing for E-Commerce Business
ITR-3 or ITR-6 for e-commerce sellers with accurate income computation, GST reconciliation, TCS credit claim, depreciation on assets, and all applicable business deductions.
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GST Notice Response for Marketplace Sellers
E-commerce sellers frequently receive scrutiny on TCS credits, GSTR-1 vs GSTR-3B mismatches, and place of supply issues. We draft and file responses with supporting reconciliation statements.
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D2C Brand Compliance — Shopify, WooCommerce
GST on D2C sales through own website, Razorpay/PayU payment gateway reconciliation, accounting for returns and chargebacks, and compliance for multi-state delivery. FEMA compliance for cross-border D2C sales.
How We Work

Simple Process

01
Platform Access
You grant us view access to your Seller Central / marketplace dashboards. We pull monthly settlement statements and reconcile them.
02
Monthly Reconciliation
Sales, returns, TCS, platform fees, and advertising reconciled with your books. Any discrepancies flagged within the first week of every month.
03
GST Return Filing
GSTR-1 and GSTR-3B filed by due dates. TCS credits and ITC claimed correctly.
04
MIS Report
Monthly profit report by platform and SKU category. Useful for pricing decisions and channel optimisation.
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Annual Compliance
GSTR-9, ITR, and financial statements prepared and filed annually.
Common Questions

Frequently Asked Questions

Yes. All sellers selling through e-commerce platforms like Amazon, Flipkart, Meesho, or any marketplace are required to register for GST regardless of their turnover. The normal GST exemption threshold (Rs.40 lakh for goods, Rs.20 lakh for services) does not apply to marketplace sellers. This is because the marketplace operator (Amazon/Flipkart) deducts TCS and requires a GSTIN to deposit it against your account. Registration must be obtained before you start selling on any marketplace.
TCS — Tax Collected at Source — under GST (Section 394 of the IGST Act, previously Section 52 of CGST Act) requires e-commerce operators to collect 1% of the net taxable sales made through their platform and deposit it with the government. This TCS appears as a credit in your Electronic Cash Ledger on the GST portal (Form 26AS for GST) and can be used against your GST liability. If your outward GST liability is lower than the TCS collected, the excess becomes a refund. Reconciling TCS across multiple platforms is complex and is a common source of errors.
E-commerce sellers can claim ITC on: GST paid on advertising spend (Amazon Sponsored Ads, Flipkart Ads), packaging materials, warehouse rent and services, courier and logistics charges (if GST is charged), CA and professional fees, platform subscription fees (if GST is applicable), and office expenses. ITC cannot be claimed on personal expenses or items used for personal consumption. ITC is available only if the vendor has filed their GST returns correctly and your GSTR-2B reflects the purchase.
If Amazon is storing your inventory in its FCs (Fulfilment Centres) in multiple states, you are required to register for GST in each state where your inventory is held. Amazon's FBA (Fulfilled by Amazon) model triggers a mandatory multi-state registration requirement because goods move between states from the FC. If you are shipping directly from your own warehouse in one state, only one-state registration is needed. We help assess your FC footprint and manage multi-state registrations accordingly.
Yes. D2C brands selling through their own website (Shopify, WooCommerce) have a different compliance profile than marketplace sellers — there is no TCS deduction, you are responsible for collecting and remitting GST directly on each sale, payment gateway reconciliation is manual, and returns/chargebacks must be handled through credit notes. For brands also selling to overseas customers, FEMA compliance for receipt of foreign exchange and Form 15CA/15CB for repatriation may be required. We handle the full D2C compliance stack.
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Complete Guide

GST & Accounting for E-Commerce Businesses in India

E-commerce businesses in India face a unique and complex GST framework. Under Section 9(5) of the CGST Act, Electronic Commerce Operators (ECOs) such as Swiggy, Zomato, Ola, and Uber must pay GST on behalf of certain service providers listed on their platform — shifting the tax liability from the supplier to the platform. Section 52 requires ECOs to collect TCS (Tax Collected at Source) at 1% of the net taxable supply made through the platform and deposit it with the government, filing Form GSTR-8 monthly.

For sellers on Amazon, Flipkart, Meesho, or other marketplaces, GST registration is mandatory regardless of turnover — there is no threshold exemption for inter-state e-commerce sales. Sellers must charge GST at the applicable rate on all supplies, file GSTR-1 and GSTR-3B monthly, and reconcile their marketplace sales data (available from seller portals) with GSTR-2B for ITC claims. The mismatch between marketplace-reported sales and GST returns is a common scrutiny trigger — monthly reconciliation is essential.

E-invoice (e-invoicing under IRP) is mandatory for e-commerce sellers with aggregate turnover exceeding ₹5 crore. All B2B invoices must be reported on the Invoice Registration Portal (IRP) and an IRN (Invoice Reference Number) and QR code affixed. B2C invoices require a QR code for turnover above ₹500 crore. Accounting for e-commerce requires accurate categorisation of marketplace commissions, returns and refunds, promotional credits, shipping charges, and TCS deducted by the platform — all reconciled to monthly settlements.

Shahi & Co. provides specialised GST and accounting services for Amazon, Flipkart, Meesho, Nykaa, and other marketplace sellers — including monthly GSTR-1/3B filing, marketplace reconciliation, e-invoice setup, annual GSTR-9/9C filing, and full accounting on cloud-based platforms. Contact us for a free GST health check for your e-commerce business.

Get in Touch

Get Your E-Commerce Compliance Right Today

Share your platforms and monthly volumes. We will set up a compliance structure that keeps your GST, TCS, and accounting clean every month.

💬 WhatsApp Us ✉ Write to Us
📞 +91-9999 361 351
✉ info@shahiandco.in
📍 Pushp Vihar, New Delhi – 110 062