Selling products online via marketplaces like Amazon India, Flipkart, Meesho, or Nykaa offers unprecedented reach. However, e-commerce sellers are subject to the strictest indirect tax oversight in India.
Unlike offline brick-and-mortar retailers who file basic monthly returns, online sellers must account for Tax Collected at Source (TCS) under Section 52, reconcile marketplace settlement sheets against GSTR-1, claim credit for customer returns across state borders, and obtain multi-state GSTINs for Fulfilled by Amazon (FBA) or Flipkart Advantage warehouses.
In this guide, we provide a complete compliance checklist and monthly calendar designed specifically for Indian e-commerce merchants.
Free E-Commerce Financial Calculators
- Calculate marketplace TCS deductions and reconcile net settlement amounts with our E-Commerce TCS Calculator.
- Model marketplace referral fees, shipping charges, and net cash margins with our Amazon / Flipkart Seller Payout Calculator.
E-Commerce GST Compliance Calendar (Monthly Deadlines)
| Date | Statutory Filing / Action | Marketplace Relevance | Notes |
|---|---|---|---|
| 10th of every month | Form GSTR-8 filed by E-Commerce Platforms | Amazon, Flipkart, Meesho file GSTR-8 detailing net sales & TCS deducted from you | Data flows to your GST portal |
| 11th of every month | Form GSTR-1 (Outward Supplies) | Mandatory deadline for sellers to report state-wise B2C and B2B sales | Late filing blocks GSTR-3B |
| 14th of every month | Accept TCS Credit in GST Portal | Navigate to Services → Returns → TDS and TCS Received | Credits flow to your Electronic Cash Ledger |
| 20th of every month | Form GSTR-3B (Payment of Tax) | Discharge net tax liability using available ITC and claimed TCS credits | Strict late fees and interest apply past due date |
| Quarterly / Annual | FBA Warehouse Inventory Reconciliation | Match physical warehouse stock in other states against ERP stock registers | Avoid stock shortage notices |
The 5-Point E-Commerce Compliance Checklist
1. Section 52 TCS Deduction & Claiming Workflow
Under Section 52 of the CGST Act, e-commerce operators deduct Tax Collected at Source (TCS) at the rate of 0.5% (0.25% CGST + 0.25% SGST) or 0.5% IGST on the net value of taxable supplies made through their platform.
- How to Recover Your Money: Marketplace TCS does not sit in a vacuum. Once Amazon/Flipkart files Form GSTR-8 on the 10th:
- Log in to
gst.gov.in. - Navigate to Services → Returns → TDS and TCS Credit Received.
- Review the auto-drafted net sales and TCS deductions, and click Accept.
- The accepted TCS amount is instantly credited to your Electronic Cash Ledger, which you can use directly to pay your GSTR-3B taxes or claim as a cash refund!
- Log in to
2. Fulfilled by Amazon (FBA) & Principal Place of Business (PPoB / APoB)
If you enroll in Amazon FBA or Flipkart Smart Fulfillment to offer Prime 1-day delivery, your inventory is physically stored in marketplace fulfillment centers located in different states (e.g., Haryana, Karnataka, Telangana, Maharashtra).
- Statutory Rule: You cannot store inventory in another state without obtaining a GST registration in that state.
- The Process: You must obtain a separate GSTIN in each state where an FBA warehouse is located, registering Amazon/Flipkart’s warehouse as an Additional Place of Business (APoB) using their formal consent letter and municipal trade license.
3. State-Wise B2C Reporting (Table 7 of GSTR-1)
When selling to end-consumers across India (B2C):
- Every sale must be reported based on the Place of Supply (POS), which is the delivery location of the customer.
- Under Table 7 of GSTR-1, you must disclose gross inter-state supplies state-by-state at respective tax rates (e.g., sales to Uttar Pradesh at 18%, sales to Tamil Nadu at 5%).
4. Handling High Customer Return Rates (RTO)
High Return-to-Origin (RTO) and customer return rates (often 20% to 35% in fashion and footwear) create significant accounting headaches:
- When a customer returns an item, the marketplace issues a negative credit adjustment in their settlement report.
- GST Reconciliation: In your GSTR-1, outward sales must be reported net of sales returns / credit notes. If your credit notes in a particular state exceed fresh sales in a given month, the net negative figure can be carried forward to subsequent months.
5. Reconciling Marketplace Inward Fee Invoices
Amazon and Flipkart issue monthly B2B tax invoices to you for:
- Marketplace Referral Fees & Closing Fees
- FBA Pick & Pack Fees and Storage Fees
- In-platform Advertising / Sponsored Product Ads
- Logistics & Shipping Charges
Ensure these inward invoices appear in your GSTR-2B so your business claims the full 18% Input Tax Credit on these platform expenses.
Frequently Asked Questions (FAQs)
Can small e-commerce sellers with turnover below ₹40 Lakhs sell without GST?
Under recent GST Council relaxations, intra-state sellers with turnover below the threshold (₹40L for goods) can sell goods through e-commerce operators without mandatory GST registration, provided they obtain an Enrolment Number on the GST portal. However, these unregistered sellers cannot make inter-state supplies and cannot store goods in out-of-state FBA warehouses.
What should I do if Amazon’s GSTR-8 figures do not match my sales register?
If there is a variance between Amazon’s reported GSTR-8 sales and your internal sales reports (often due to transit timing differences at month-end), accept the undisputed records on the portal and claim the variance in the subsequent month’s reconciliation.